<PAGE>   1
      As filed with the Securities and Exchange Commission on June 25, 1997
                                                    Registration No. 333-

===============================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                             ----------------------

                                    FORM S-8
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

                         Aurora Biosciences Corporation
             (Exact name of Registrant as specified in its charter)

                             ----------------------

            Delaware                                       33-0669859
  (State or other jurisdiction                          (I.R.S. Employer
of incorporation or organization)                     Identification Number)

                          11149 North Torrey Pines Road
                           La Jolla, California 92037
                                 (619) 452-5000
    (Address, including zip code, and telephone number, including area code,
                  of Registrant's principal executive offices)

                             ----------------------

                                 1996 STOCK PLAN
                          EMPLOYEE STOCK PURCHASE PLAN
                    NON-EMPLOYEE DIRECTORS' STOCK OPTION PLAN
                            (Full title of the plans)

                             ----------------------

                                 Timothy J. Rink
          Chairman of the Board, President and Chief Executive Officer
                         AURORA BIOSCIENCES CORPORATION
                          11149 North Torrey Pines Road
                           La Jolla, California 92037
                                 (619) 452-5000
            (Name, address, including zip code, and telephone number,
                   including area code, of agent for service)

                             ----------------------

                                   Copies to:

                              Thomas A. Coll, Esq.
                              Eric J. Loumeau, Esq.
                               COOLEY GODWARD LLP
                        4365 Executive Drive, Suite 1100
                               San Diego, CA 92121
                                 (619) 550-6000

                             ----------------------

<PAGE>   2
<TABLE>
<CAPTION>
                                          CALCULATION OF REGISTRATION FEE
===================================================================================================================================
                                                                             Proposed Maximum   Proposed Maximum                   
                  Title of Securities                        Amount to        Offering Price        Aggregate          Amount of   
                    to be Registered                       be Registered      Per Share (1)    Offering Price (1)  Registration Fee
-----------------------------------------------------------------------------------------------------------------------------------
<S>                                                         <C>                 <C>               <C>                  <C>   
  Common Stock, $.001 par value                              2,207,528           $10.9375          $18,039,632          $5,467
===================================================================================================================================
</TABLE>

(1)  Estimated solely for the purpose of calculating the amount of the
     registration fee pursuant to Rule 457. The price per share and aggregate
     offering price are based upon (a) the actual exercise price for shares
     subject to outstanding stock options previously granted under the
     Registrant's 1996 Stock Plan and Non-Employee Directors' Stock Option Plan
     and (b) the average of the high and low sales prices of Registrant's Common
     Stock on June 23, 1997, as reported on the Nasdaq National Market, for
     shares issuable under the Company's Employee Stock Purchase Plan, 1996
     Stock Plan and Non-Employee Directors' Stock Option Plan. The following
     chart shows the calculation of the registration fee.
<TABLE>
<CAPTION>
---------------------------------------------------------------------------------------------------------------------
                                                                                                    Aggregate
              Type of Shares                    Number of Shares      Offering Price Per Share     Offering Price
---------------------------------------------------------------------------------------------------------------------
<S>                                                  <C>                       <C>                      <C> 
Common Stock issuable pursuant to                    4,000                     $.0875                   $350
outstanding options under the 1996 Stock
Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable pursuant to                    50,736                     $.375                  $19,026
outstanding options under the 1996 Stock
Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable pursuant to                   118,584                     $.75                   $88,938
outstanding options under the 1996 Stock
Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable pursuant to                   311,200                     $1.50                 $466,800
outstanding options under the 1996 Stock
Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable pursuant to                    19,200                     $2.40                  46,080
outstanding options under the 1996 Stock
Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable pursuant to                    58,200                     $3.00                 $174,600
outstanding options under the 1996 Stock
Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable under the 1996               1,005,608                  $10.9375               $10,998,838
Stock Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable pursuant to                    80,000                     $1.50                 $120,000
outstanding options under the
Non-Employee Directors' Stock Option Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable under the                     160,000                   $10.9375               $1,750,000
Non-Employee Directors' Stock Option Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable under the Employee            400,000                   $10.9375               $4,375,000
Stock Purchase Plan
---------------------------------------------------------------------------------------------------------------------
</TABLE>
<PAGE>   3
                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 3.  Incorporation of Documents by Reference.

         The prospectus contained in the Form S-1 Registration Statement (No.
333-23407) filed by Aurora Biosciences Corporation (the "Registrant") with the
Securities and Exchange Commission (the "Commission") on March 14, 1997, as
amended through the date hereof (the "Form S-1"), is hereby incorporated by
reference into this Registration Statement. The Registrant has not filed, and
has not been required to file, any reports pursuant to Section 13 or 15(d) of
the Securities Exchange Act of 1934, as amended (the "Exchange Act"), as of the
date hereof. A description of the Registrant's Common Stock which is contained
in the Form S-1, including any amendment or reports filed for the purpose of
updating such description, is hereby incorporated by reference into this
Registration Statement. All documents filed by the Registrant with the
Commission pursuant to Sections 13(a), 13(c), 14 or 15(d) of the Exchange Act
after the date of this Registration Statement and prior to the filing of a
post-effective amendment which indicates that all securities offered have been
sold or which deregisters all securities then remaining unsold shall be deemed
to be incorporated by reference into this Registration Statement and to be a
part hereof from the date of filing of such documents. Any statement contained
in a document incorporated by reference herein shall be deemed to be modified or
superseded for purposes of this Registration Statement to the extent that a
statement contained herein or in any other subsequently filed document which
also is or is deemed to be incorporated by reference herein modifies or
supersedes such statement. Any statement so modified or superseded shall not be
deemed, except as so modified or superseded, to constitute a part of this
Registration Statement.

Item 4.  Description of Securities.

         Not applicable.

Item 5.  Interests of Named Experts and Counsel.

         The validity of the shares of Common Stock offered hereby will be
passed upon for the Company by Cooley Godward LLP, San Diego, California. As of
the date of this Prospectus, certain members and associates of Cooley Godward
own an aggregate of 30,074 shares of Common Stock through an investment
partnership.

Item 6.  Indemnification of Directors and Officers.

         Under Section 145 of the Delaware General Corporation Law, the
Registrant has broad powers to indemnify its Directors and officers against
liabilities they may incur in such capacities, including liabilities under the
Securities Act.

                                       1.
<PAGE>   4
         The Registrant's Restated Certificate of Incorporation and Amended and
Restated Bylaws include provisions to (i) eliminate the personal liability of
its directors for monetary damages resulting from breaches of their fiduciary
duty to the extent permitted by Section 102(b)(7) of the General Corporation Law
of Delaware (the "Delaware Law") and (ii) require the Registrant to indemnify
its Directors and officers to the fullest extent permitted by Section 145 of the
Delaware Law, including circumstances in which indemnification is otherwise
discretionary. Pursuant to Section 145 of the Delaware Law, a corporation
generally has the power to indemnify its present and former directors, officers,
employees and agents against expenses incurred by them in connection with any
suit to which they are or are threatened to be made, a party by reason of their
serving in such positions so long as they acted in good faith and in a manner
they reasonably believed to be in or not opposed to, the best interests of the
corporation and with respect to any criminal action, they had no reasonable
cause to believe their conduct was unlawful. The Registrant believes that these
provisions are necessary to attract and retain qualified persons as Directors
and officers. These provisions do not eliminate the Directors' duty of care,
and, in appropriate circumstances, equitable remedies such as injunctive or
other forms of non-monetary relief will remain available under Delaware Law. In
addition, each Director will continue to be subject to liability for breach of
the Director's duty of loyalty to the Registrant, for acts or omissions not in
good faith or involving intentional misconduct, for knowing violations of law,
for acts or omissions that the Director believes to be contrary to the best
interests of the Registrant or its stockholders, for any transaction from which
the Director derived an improper personal benefit, for acts or omissions
involving a reckless disregard for the Director's duty to the Registrant or its
stockholders when the Director was aware or should have been aware of a risk of
serious injury to the Registrant or its stockholders, for acts or omissions that
constitute an unexcused pattern of inattention that amounts to an abdication of
the Director's duty to the Registrant or its stockholders, for improper
transactions between the Director and the Registrant and for improper
distributions to stockholders and loans to Directors and officers. The provision
also does not affect a Director's responsibilities under any other law, such as
the federal securities law or state or federal environmental laws.

         The Registrant has entered into indemnity agreements with each of its
Directors and executive officers that require the Registrant to indemnify such
persons against expenses, judgments, fines, settlements and other amounts
incurred (including expenses of a derivative action) in connection with any
proceeding, whether actual or threatened, to which any such person may be made a
party by reason of the fact that such person is or was a Director or an
executive officer of the Registrant or any of its affiliated enterprises,
provided that such person acted in good faith and in a manner such person
reasonably believed to be in or not opposed to the best interests of the
Registrant and, with respect to any criminal proceeding, had no reasonable cause
to believe his conduct was unlawful. The indemnification agreements also set
forth certain procedures that will apply in the event of a claim for
indemnification thereunder. The Registrant has entered into similar indemnity
agreements with certain of its key employees.

         At present, there is no pending litigation or proceeding involving a
Director, officer or key employee of the Registrant as to which indemnification
is being sought nor is the Registrant aware of any threatened litigation that
may result in claims for indemnification by any officer or Director.


                                       2.
<PAGE>   5
         The Registrant has an insurance policy covering the officers and
Directors of the Registrant with respect to certain liabilities, including
liabilities arising under the Securities Act or otherwise.

Item 7.  Exemption from Registration Claimed.

         Not applicable.

Item 8.  Exhibits.
<TABLE>
<CAPTION>
Exhibit No.  Description
----------   -----------
<S>          <C>
*    4.1     Restated Certificate of Incorporation.
*    4.2     Restated Bylaws.
*    4.3     Form of Common Stock Certificate.
     5.1     Opinion of Cooley Godward LLP.
     23.1    Consent of Ernst & Young LLP, Independent Auditors.
     23.2    Consent of Cooley Godward LLP.  Reference is made to Exhibit 5.1.
     24.1    Power of Attorney.  Reference is made to page 6.
*    99.1    Registrant's 1996 Stock Plan, as amended and restated (the "1996
             Stock Plan").
*    99.2    Form of Incentive Stock Option Agreement under the 1996 Stock
             Plan.
*    99.3    Form of Non-Statutory Stock Option Agreement under the 1996 Stock
             Plan.
*    99.4    Form of Restricted Stock Purchase Agreement under the 1996 Stock
             Plan.
*    99.5    Registrant's Employee Stock Purchase Plan and related offering
             document.
*    99.6    Registrant's Non-Employee Directors' Stock Option Plan.
*    99.7    Form of Non-Statutory Stock Option under Registrant's Non-Employee
             Directors' Stock Option Plan.
</TABLE>
 -----------------------

 *       Filed as an exhibit to Registration  Statement on Form S-1 (No.
         333-23407) originally filed on March 14, 1997, as amended through the
         date hereof, and incorporated herein by reference.

                                       3.
<PAGE>   6
Item 9.  Undertakings.

1.       The undersigned Registrant hereby undertakes:


         (a) To file, during any period in which offers or sales are being made,
a post-effective amendment to this Registration Statement:


                  (i)  To include any prospectus required by Section 10(a)(3)
of the Securities Act of 1933;


                  (ii) To reflect in the prospectus any facts or events arising
after the effective date of the Registration Statement (or the most recent
post-effective amendment thereof) which, individually or in the aggregate,
represent a fundamental change in the information set forth in the Registration
Statement. Notwithstanding the foregoing, any increase or decrease in volume of
securities offered (if the total dollar value of securities offered would not
exceed that which was registered) and any deviation from the low or high end of
the estimated maximum offering range may be reflected in the form of prospectus
filed with the Commission pursuant to Rule 424(b) if, in the aggregate, the
changes in volume and price represent no more than a 20% change in the maximum
aggregate offering price set forth in the "Calculation of Registration Fee"
table in the effective Registration Statement;


                  (iii) To include any material information with respect to the
plan of distribution not previously disclosed in the Registration Statement or
any material change to such information in the Registration Statement;


         Provided, however, that paragraphs (1)(a)(i) and (1)(a)(ii) above do
not apply if the information required to be included in a post-effective
amendment by those paragraphs is contained in periodic reports filed with or
furnished to the Commission by the Registrant pursuant to Section 13 or Section
15(d) of the Securities Exchange Act of 1934 that are incorporated by reference
in this Registration Statement.


         (b) That, for the purpose of determining any liability under the
Securities Act of 1934, each such post-effective amendment shall be deemed to be
a new registration statement relating to the securities offered therein, and the
offering of such securities at that time shall be deemed to be the initial bona
fide offering thereof.

                                       4.
<PAGE>   7
         (c) To remove from registration by means of a post-effective amendment
any of the securities being registered which remain unsold at the termination of
the offering.


2. The undersigned Registrant hereby undertakes that, for purposes of
determining any liability under the Securities Act of 1933, each filing of the
Registrant's annual report pursuant to Section 13(a) or Section 15(d) of the
Exchange Act of 1934 (and, where applicable, each filing of an employee benefit
plan's annual report pursuant to Section 15(d) of the Exchange Act of 1934) that
is incorporated by reference in the Registration Statement shall be deemed to be
a new registration statement relating to the securities offered therein, and the
offering of such securities at that time shall be deemed to be the initial bona
fide offering thereof.


3. Insofar as indemnification for liabilities arising under the Securities Act
of 1933 may be permitted to directors, officers and controlling persons of the
Registrant pursuant to the foregoing provisions, or otherwise, the Registrant
has been advised that in the opinion of the Securities and Exchange Commission
such indemnification is against public policy as expressed in the Act, and is,
therefore, unenforceable. In the event that a claim for indemnification against
such liabilities (other than the payment by the Registrant of expenses incurred
or paid by a director, officer or controlling person of the Registrant in the
successful defense of any action, suit or proceeding) is asserted by such
director, officer or controlling person in connection with the securities being
registered, the Registrant will, unless in the opinion of its counsel the matter
has been settled by controlling precedent, submit to a court of appropriate
jurisdiction the question whether such indemnification by it is against public
policy as expressed in the Act and will be governed by the final adjudication of
such issue.


                                       5.
<PAGE>   8
                                   SIGNATURES

      Pursuant to the requirements of the Securities Act of 1933, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-8 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of San Diego, State of California, on June 24, 1997.

                                   AURORA BIOSCIENCES CORPORATION

                                   By:  /s/ Timothy J. Rink
                                       ----------------------------------------
                                       Timothy J. Rink
                                       President and Chief Executive Officer

                                POWER OF ATTORNEY

      KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature
appears below constitutes and appoints Timothy J. Rink, his true and lawful
attorney-in-fact and agent, with full power of substitution and resubstitution,
for him and in his name, place and stead, in any and all capacities, to sign any
and all amendments (including post-effective amendments, exhibits thereto and
other documents in connection with) to this Registration Statement, and to file
the same, with all exhibits thereto, and other documents in connection
therewith, with the Securities and Exchange Commission, granting unto said
attorney-in-fact and agent full power and authority to do and perform each and
every act and thing requisite and necessary to be done in connection therewith,
as fully to all intents and purposes as he or she might or could do in person,
hereby ratifying and confirming all that said attorney-in-fact and agent, or his
substitutes or substitute, may lawfully do or cause to be done by virtue hereof.

      Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed by the following persons in the
capacities and on the dates indicated.

<TABLE>
<CAPTION>
Signature                                      Title                                                   Date
---------                                      -----                                                   ----
<S>                                            <C>                                                     <C>
  /s/ Timothy J. Rink                          Chairman of the Board, President and Chief              June 24, 1997
-------------------------------------------    Executive Officer (Principal Executive 
Timothy J. Rink, M.A., M.D., Sc.D.             Officer)                               
                                               


  /s/ Deborah J. Tower                         Senior Director of Finance and Administration           June 24, 1997
-------------------------------------------    (Principal Financial and Accounting Officer)
Deborah J. Tower                               


  /s/ J. Gordon Foulkes, Ph.D.                 Director                                                June 24, 1997
-------------------------------------------
J. Gordon Foulkes, Ph.D.


  /s/ James C. Blair                           Director                                                June 24, 1997
-------------------------------------------
James C. Blair, Ph.D.


  /s/ Kevin J. Kinsella                        Director                                                June 24, 1997
-------------------------------------------
Kevin J. Kinsella


  /s/ Hugh Y. Rienhoff                         Director                                                June 24, 1997
-------------------------------------------
Hugh Y. Rienhoff, Jr., M.D.


  /s/ Lubert Stryer                            Director                                                June 24, 1997
-------------------------------------------
Lubert Stryer, M.D.


  /s/ Timothy J. Wollaeger                     Director                                                June 24, 1997
-------------------------------------------
Timothy J. Wollaeger
</TABLE>
                                       6.
<PAGE>   9

                                  EXHIBIT INDEX
<TABLE>
<CAPTION>
                                                                                                       Sequential
     Exhibit No.  Description                                                                           Page No. 
     ----------   ------------                                                                         ----------
<S>               <C>
*    4.1          Restated Certificate of Incorporation.
*    4.2          Restated Bylaws.
*    4.3          Form of Common Stock Certificate.
     5.1          Opinion of Cooley Godward LLP.
     23.1         Consent of Ernst & Young LLP, Independent Auditors.
     23.2         Consent of Cooley Godward LLP.  Reference is made to Exhibit 5.1.
     24.1         Power of Attorney.  Reference is made to page 6.
*    99.1         Registrant's 1996 Stock Plan, as amended and restated (the "1996 Stock Plan").
*    99.2         Form of Incentive Stock Option Agreement under the 1996 Stock Plan.

*    99.3         Form of Non-Statutory Stock Option Agreement under the 1996 Stock Plan.

*    99.4         Form of Restricted Stock Purchase Agreement under the 1996 Stock Plan.

*    99.5         Registrant's Employee Stock Purchase Plan and related offering document.

*    99.6         Registrant's Non-Employee Directors' Stock Option Plan.

*    99.7         Form of Non-Statutory Stock Option under Registrant's Non-Employee Directors' Stock Option Plan.
</TABLE>
 -----------------------

 * Filed as an exhibit to Registration  Statement on Form S-1 (No.  333-23407)
   originally filed on March 14, 1997, as amended through the date hereof, and
   incorporated herein by reference.


                                       7.
[{"type": "S-8", "sequence": "1", "description": "FORM S-8", "secsgml_size_bytes": 26510}]
{"company-data": {"conformed-name": "AURORA BIOSCIENCES CORP", "cik": "0001010919", "assigned-sic": "8731", "irs-number": "330669859", "state-of-incorporation": "DE", "fiscal-year-end": "1231"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-30039", "film-number": "97629767"}, "business-address": {"street1": "11149 N TORREY PINES RD", "city": "LA JOLLA", "state": "CA", "zip": "92037", "phone": "6194255000"}, "mail-address": {"street1": "11149 NORTH TORREY PINES ROAD", "city": "LA JOLLA", "state": "CA", "zip": "92037"}}
1
      As filed with the Securities and Exchange Commission on June 25, 1997
                                                    Registration No. 333-

===============================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             Washington, D.C. 20549

                             ----------------------

                                    FORM S-8
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

                         Aurora Biosciences Corporation
             (Exact name of Registrant as specified in its charter)

                             ----------------------

            Delaware                                       33-0669859
  (State or other jurisdiction                          (I.R.S. Employer
of incorporation or organization)                     Identification Number)

                          11149 North Torrey Pines Road
                           La Jolla, California 92037
                                 (619) 452-5000
    (Address, including zip code, and telephone number, including area code,
                  of Registrant's principal executive offices)

                             ----------------------

                                 1996 STOCK PLAN
                          EMPLOYEE STOCK PURCHASE PLAN
                    NON-EMPLOYEE DIRECTORS' STOCK OPTION PLAN
                            (Full title of the plans)

                             ----------------------

                                 Timothy J. Rink
          Chairman of the Board, President and Chief Executive Officer
                         AURORA BIOSCIENCES CORPORATION
                          11149 North Torrey Pines Road
                           La Jolla, California 92037
                                 (619) 452-5000
            (Name, address, including zip code, and telephone number,
                   including area code, of agent for service)

                             ----------------------

                                   Copies to:

                              Thomas A. Coll, Esq.
                              Eric J. Loumeau, Esq.
                               COOLEY GODWARD LLP
                        4365 Executive Drive, Suite 1100
                               San Diego, CA 92121
                                 (619) 550-6000

                             ----------------------
2
CALCULATION OF REGISTRATION FEE
===================================================================================================================================
                                                                             Proposed Maximum   Proposed Maximum                   
                  Title of Securities                        Amount to        Offering Price        Aggregate          Amount of   
                    to be Registered                       be Registered      Per Share (1)    Offering Price (1)  Registration Fee
-----------------------------------------------------------------------------------------------------------------------------------
Common Stock, $.001 par value                              2,207,528           $10.9375          $18,039,632          $5,467
===================================================================================================================================
(1)  Estimated solely for the purpose of calculating the amount of the
     registration fee pursuant to Rule 457. The price per share and aggregate
     offering price are based upon (a) the actual exercise price for shares
     subject to outstanding stock options previously granted under the
     Registrant's 1996 Stock Plan and Non-Employee Directors' Stock Option Plan
     and (b) the average of the high and low sales prices of Registrant's Common
     Stock on June 23, 1997, as reported on the Nasdaq National Market, for
     shares issuable under the Company's Employee Stock Purchase Plan, 1996
     Stock Plan and Non-Employee Directors' Stock Option Plan. The following
     chart shows the calculation of the registration fee.
---------------------------------------------------------------------------------------------------------------------
                                                                                                    Aggregate
              Type of Shares                    Number of Shares      Offering Price Per Share     Offering Price
---------------------------------------------------------------------------------------------------------------------
Common Stock issuable pursuant to                    4,000                     $.0875                   $350
outstanding options under the 1996 Stock
Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable pursuant to                    50,736                     $.375                  $19,026
outstanding options under the 1996 Stock
Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable pursuant to                   118,584                     $.75                   $88,938
outstanding options under the 1996 Stock
Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable pursuant to                   311,200                     $1.50                 $466,800
outstanding options under the 1996 Stock
Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable pursuant to                    19,200                     $2.40                  46,080
outstanding options under the 1996 Stock
Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable pursuant to                    58,200                     $3.00                 $174,600
outstanding options under the 1996 Stock
Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable under the 1996               1,005,608                  $10.9375               $10,998,838
Stock Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable pursuant to                    80,000                     $1.50                 $120,000
outstanding options under the
Non-Employee Directors' Stock Option Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable under the                     160,000                   $10.9375               $1,750,000
Non-Employee Directors' Stock Option Plan
---------------------------------------------------------------------------------------------------------------------

Common Stock issuable under the Employee            400,000                   $10.9375               $4,375,000
Stock Purchase Plan
---------------------------------------------------------------------------------------------------------------------
3
                                     PART II

               INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 3.  Incorporation of Documents by Reference.

         The prospectus contained in the Form S-1 Registration Statement (No.
333-23407) filed by Aurora Biosciences Corporation (the "Registrant") with the
Securities and Exchange Commission (the "Commission") on March 14, 1997, as
amended through the date hereof (the "Form S-1"), is hereby incorporated by
reference into this Registration Statement. The Registrant has not filed, and
has not been required to file, any reports pursuant to Section 13 or 15(d) of
the Securities Exchange Act of 1934, as amended (the "Exchange Act"), as of the
date hereof. A description of the Registrant's Common Stock which is contained
in the Form S-1, including any amendment or reports filed for the purpose of
updating such description, is hereby incorporated by reference into this
Registration Statement. All documents filed by the Registrant with the
Commission pursuant to Sections 13(a), 13(c), 14 or 15(d) of the Exchange Act
after the date of this Registration Statement and prior to the filing of a
post-effective amendment which indicates that all securities offered have been
sold or which deregisters all securities then remaining unsold shall be deemed
to be incorporated by reference into this Registration Statement and to be a
part hereof from the date of filing of such documents. Any statement contained
in a document incorporated by reference herein shall be deemed to be modified or
superseded for purposes of this Registration Statement to the extent that a
statement contained herein or in any other subsequently filed document which
also is or is deemed to be incorporated by reference herein modifies or
supersedes such statement. Any statement so modified or superseded shall not be
deemed, except as so modified or superseded, to constitute a part of this
Registration Statement.

Item 4.  Description of Securities.

         Not applicable.

Item 5.  Interests of Named Experts and Counsel.

         The validity of the shares of Common Stock offered hereby will be
passed upon for the Company by Cooley Godward LLP, San Diego, California. As of
the date of this Prospectus, certain members and associates of Cooley Godward
own an aggregate of 30,074 shares of Common Stock through an investment
partnership.

Item 6.  Indemnification of Directors and Officers.

         Under Section 145 of the Delaware General Corporation Law, the
Registrant has broad powers to indemnify its Directors and officers against
liabilities they may incur in such capacities, including liabilities under the
Securities Act.

                                       1.
4
         The Registrant's Restated Certificate of Incorporation and Amended and
Restated Bylaws include provisions to (i) eliminate the personal liability of
its directors for monetary damages resulting from breaches of their fiduciary
duty to the extent permitted by Section 102(b)(7) of the General Corporation Law
of Delaware (the "Delaware Law") and (ii) require the Registrant to indemnify
its Directors and officers to the fullest extent permitted by Section 145 of the
Delaware Law, including circumstances in which indemnification is otherwise
discretionary. Pursuant to Section 145 of the Delaware Law, a corporation
generally has the power to indemnify its present and former directors, officers,
employees and agents against expenses incurred by them in connection with any
suit to which they are or are threatened to be made, a party by reason of their
serving in such positions so long as they acted in good faith and in a manner
they reasonably believed to be in or not opposed to, the best interests of the
corporation and with respect to any criminal action, they had no reasonable
cause to believe their conduct was unlawful. The Registrant believes that these
provisions are necessary to attract and retain qualified persons as Directors
and officers. These provisions do not eliminate the Directors' duty of care,
and, in appropriate circumstances, equitable remedies such as injunctive or
other forms of non-monetary relief will remain available under Delaware Law. In
addition, each Director will continue to be subject to liability for breach of
the Director's duty of loyalty to the Registrant, for acts or omissions not in
good faith or involving intentional misconduct, for knowing violations of law,
for acts or omissions that the Director believes to be contrary to the best
interests of the Registrant or its stockholders, for any transaction from which
the Director derived an improper personal benefit, for acts or omissions
involving a reckless disregard for the Director's duty to the Registrant or its
stockholders when the Director was aware or should have been aware of a risk of
serious injury to the Registrant or its stockholders, for acts or omissions that
constitute an unexcused pattern of inattention that amounts to an abdication of
the Director's duty to the Registrant or its stockholders, for improper
transactions between the Director and the Registrant and for improper
distributions to stockholders and loans to Directors and officers. The provision
also does not affect a Director's responsibilities under any other law, such as
the federal securities law or state or federal environmental laws.

         The Registrant has entered into indemnity agreements with each of its
Directors and executive officers that require the Registrant to indemnify such
persons against expenses, judgments, fines, settlements and other amounts
incurred (including expenses of a derivative action) in connection with any
proceeding, whether actual or threatened, to which any such person may be made a
party by reason of the fact that such person is or was a Director or an
executive officer of the Registrant or any of its affiliated enterprises,
provided that such person acted in good faith and in a manner such person
reasonably believed to be in or not opposed to the best interests of the
Registrant and, with respect to any criminal proceeding, had no reasonable cause
to believe his conduct was unlawful. The indemnification agreements also set
forth certain procedures that will apply in the event of a claim for
indemnification thereunder. The Registrant has entered into similar indemnity
agreements with certain of its key employees.

         At present, there is no pending litigation or proceeding involving a
Director, officer or key employee of the Registrant as to which indemnification
is being sought nor is the Registrant aware of any threatened litigation that
may result in claims for indemnification by any officer or Director.

                                       2.
5
         The Registrant has an insurance policy covering the officers and
Directors of the Registrant with respect to certain liabilities, including
liabilities arising under the Securities Act or otherwise.

Item 7.  Exemption from Registration Claimed.

         Not applicable.

Item 8.  Exhibits.
Exhibit No.  Description
----------   -----------
*    4.1     Restated Certificate of Incorporation.
*    4.2     Restated Bylaws.
*    4.3     Form of Common Stock Certificate.
     5.1     Opinion of Cooley Godward LLP.
     23.1    Consent of Ernst & Young LLP, Independent Auditors.
     23.2    Consent of Cooley Godward LLP.  Reference is made to Exhibit 5.1.
     24.1    Power of Attorney.  Reference is made to page 6.
*    99.1    Registrant's 1996 Stock Plan, as amended and restated (the "1996
             Stock Plan").
*    99.2    Form of Incentive Stock Option Agreement under the 1996 Stock
             Plan.
*    99.3    Form of Non-Statutory Stock Option Agreement under the 1996 Stock
             Plan.
*    99.4    Form of Restricted Stock Purchase Agreement under the 1996 Stock
             Plan.
*    99.5    Registrant's Employee Stock Purchase Plan and related offering
             document.
*    99.6    Registrant's Non-Employee Directors' Stock Option Plan.
*    99.7    Form of Non-Statutory Stock Option under Registrant's Non-Employee
             Directors' Stock Option Plan.
-----------------------

 *       Filed as an exhibit to Registration  Statement on Form S-1 (No.
         333-23407) originally filed on March 14, 1997, as amended through the
         date hereof, and incorporated herein by reference.

                                       3.
6
Item 9.  Undertakings.

1.       The undersigned Registrant hereby undertakes:

         (a) To file, during any period in which offers or sales are being made,
a post-effective amendment to this Registration Statement:

                  (i)  To include any prospectus required by Section 10(a)(3)
of the Securities Act of 1933;

                  (ii) To reflect in the prospectus any facts or events arising
after the effective date of the Registration Statement (or the most recent
post-effective amendment thereof) which, individually or in the aggregate,
represent a fundamental change in the information set forth in the Registration
Statement. Notwithstanding the foregoing, any increase or decrease in volume of
securities offered (if the total dollar value of securities offered would not
exceed that which was registered) and any deviation from the low or high end of
the estimated maximum offering range may be reflected in the form of prospectus
filed with the Commission pursuant to Rule 424(b) if, in the aggregate, the
changes in volume and price represent no more than a 20% change in the maximum
aggregate offering price set forth in the "Calculation of Registration Fee"
table in the effective Registration Statement;

                  (iii) To include any material information with respect to the
plan of distribution not previously disclosed in the Registration Statement or
any material change to such information in the Registration Statement;

         Provided, however, that paragraphs (1)(a)(i) and (1)(a)(ii) above do
not apply if the information required to be included in a post-effective
amendment by those paragraphs is contained in periodic reports filed with or
furnished to the Commission by the Registrant pursuant to Section 13 or Section
15(d) of the Securities Exchange Act of 1934 that are incorporated by reference
in this Registration Statement.

         (b) That, for the purpose of determining any liability under the
Securities Act of 1934, each such post-effective amendment shall be deemed to be
a new registration statement relating to the securities offered therein, and the
offering of such securities at that time shall be deemed to be the initial bona
fide offering thereof.

                                       4.
7
         (c) To remove from registration by means of a post-effective amendment
any of the securities being registered which remain unsold at the termination of
the offering.

2. The undersigned Registrant hereby undertakes that, for purposes of
determining any liability under the Securities Act of 1933, each filing of the
Registrant's annual report pursuant to Section 13(a) or Section 15(d) of the
Exchange Act of 1934 (and, where applicable, each filing of an employee benefit
plan's annual report pursuant to Section 15(d) of the Exchange Act of 1934) that
is incorporated by reference in the Registration Statement shall be deemed to be
a new registration statement relating to the securities offered therein, and the
offering of such securities at that time shall be deemed to be the initial bona
fide offering thereof.

3. Insofar as indemnification for liabilities arising under the Securities Act
of 1933 may be permitted to directors, officers and controlling persons of the
Registrant pursuant to the foregoing provisions, or otherwise, the Registrant
has been advised that in the opinion of the Securities and Exchange Commission
such indemnification is against public policy as expressed in the Act, and is,
therefore, unenforceable. In the event that a claim for indemnification against
such liabilities (other than the payment by the Registrant of expenses incurred
or paid by a director, officer or controlling person of the Registrant in the
successful defense of any action, suit or proceeding) is asserted by such
director, officer or controlling person in connection with the securities being
registered, the Registrant will, unless in the opinion of its counsel the matter
has been settled by controlling precedent, submit to a court of appropriate
jurisdiction the question whether such indemnification by it is against public
policy as expressed in the Act and will be governed by the final adjudication of
such issue.

                                       5.
8
                                   SIGNATURES

      Pursuant to the requirements of the Securities Act of 1933, the Registrant
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-8 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of San Diego, State of California, on June 24, 1997.

                                   AURORA BIOSCIENCES CORPORATION

                                   By:  /s/ Timothy J. Rink
                                       ----------------------------------------
                                       Timothy J. Rink
                                       President and Chief Executive Officer

                                POWER OF ATTORNEY

      KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature
appears below constitutes and appoints Timothy J. Rink, his true and lawful
attorney-in-fact and agent, with full power of substitution and resubstitution,
for him and in his name, place and stead, in any and all capacities, to sign any
and all amendments (including post-effective amendments, exhibits thereto and
other documents in connection with) to this Registration Statement, and to file
the same, with all exhibits thereto, and other documents in connection
therewith, with the Securities and Exchange Commission, granting unto said
attorney-in-fact and agent full power and authority to do and perform each and
every act and thing requisite and necessary to be done in connection therewith,
as fully to all intents and purposes as he or she might or could do in person,
hereby ratifying and confirming all that said attorney-in-fact and agent, or his
substitutes or substitute, may lawfully do or cause to be done by virtue hereof.

      Pursuant to the requirements of the Securities Act of 1933, this
Registration Statement has been signed by the following persons in the
capacities and on the dates indicated.
Signature                                      Title                                                   Date
---------                                      -----                                                   ----
/s/ Timothy J. Rink                          Chairman of the Board, President and Chief              June 24, 1997
-------------------------------------------    Executive Officer (Principal Executive 
Timothy J. Rink, M.A., M.D., Sc.D.             Officer)                               
                                               

  /s/ Deborah J. Tower                         Senior Director of Finance and Administration           June 24, 1997
-------------------------------------------    (Principal Financial and Accounting Officer)
Deborah J. Tower                               

  /s/ J. Gordon Foulkes, Ph.D.                 Director                                                June 24, 1997
-------------------------------------------
J. Gordon Foulkes, Ph.D.

  /s/ James C. Blair                           Director                                                June 24, 1997
-------------------------------------------
James C. Blair, Ph.D.

  /s/ Kevin J. Kinsella                        Director                                                June 24, 1997
-------------------------------------------
Kevin J. Kinsella

  /s/ Hugh Y. Rienhoff                         Director                                                June 24, 1997
-------------------------------------------
Hugh Y. Rienhoff, Jr., M.D.

  /s/ Lubert Stryer                            Director                                                June 24, 1997
-------------------------------------------
Lubert Stryer, M.D.

  /s/ Timothy J. Wollaeger                     Director                                                June 24, 1997
-------------------------------------------
Timothy J. Wollaeger
6.
9

                                  EXHIBIT INDEX
Sequential
     Exhibit No.  Description                                                                           Page No. 
     ----------   ------------                                                                         ----------
*    4.1          Restated Certificate of Incorporation.
*    4.2          Restated Bylaws.
*    4.3          Form of Common Stock Certificate.
     5.1          Opinion of Cooley Godward LLP.
     23.1         Consent of Ernst & Young LLP, Independent Auditors.
     23.2         Consent of Cooley Godward LLP.  Reference is made to Exhibit 5.1.
     24.1         Power of Attorney.  Reference is made to page 6.
*    99.1         Registrant's 1996 Stock Plan, as amended and restated (the "1996 Stock Plan").
*    99.2         Form of Incentive Stock Option Agreement under the 1996 Stock Plan.

*    99.3         Form of Non-Statutory Stock Option Agreement under the 1996 Stock Plan.

*    99.4         Form of Restricted Stock Purchase Agreement under the 1996 Stock Plan.

*    99.5         Registrant's Employee Stock Purchase Plan and related offering document.

*    99.6         Registrant's Non-Employee Directors' Stock Option Plan.

*    99.7         Form of Non-Statutory Stock Option under Registrant's Non-Employee Directors' Stock Option Plan.
-----------------------

 * Filed as an exhibit to Registration  Statement on Form S-1 (No.  333-23407)
   originally filed on March 14, 1997, as amended through the date hereof, and
   incorporated herein by reference.

                                       7.