<PAGE>   1


                         As filed with the Securities and Exchange Commission on
                                                 Registration No. 333-__________

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                                ----------------

                                    FORM S-8

                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933
                                ----------------

                            MOLECULAR DYNAMICS, INC.
             (Exact name of Registrant as specified in its charter)

         DELAWARE                                            94-3050031
 (State of incorporation)                                 (I.R.S. Employer
                                                          Identification No.)

                              928 EAST ARQUES AVE.,
                               SUNNYVALE, CA 94086
                    (Address of principal executive offices)
                             -----------------------

                        1993 EMPLOYEE STOCK PURCHASE PLAN
                            (Full title of the Plan)
                             -----------------------

                                   JAY FLATLEY
                      PRESIDENT AND CHIEF EXECUTIVE OFFICER
                            MOLECULAR DYNAMICS, INC.
                              928 EAST ARQUES AVE.,
                               SUNNYVALE, CA 94086
                                 (408) 733-1222
 (Name, address and telephone number, including area code, of agent for service)
                             -----------------------
                                    Copy to:

                                 Jeffrey Y. Suto
                                Venture Law Group
                               2800 Sand Hill Road
                          Menlo Park, California 94025
                                 (415) 854-4488

                                Page 1 of 9 Pages
                             Exhibit Index on Page 7
               (Calculation of Registration Fee on following page)
<PAGE>   2
                       CALCULATION OF REGISTRATION FEE
<TABLE>
<CAPTION>
                                                                         Proposed                Proposed
                                             Maximum                      Maximum                 Maximum               Amount of
                                            Amount to                    Offering                Aggregate            Registration
   Title of Securities to be                    be                       Price Per               Offering                 Fee
          Registered                       Registered(1)                   Share                   Price
----------------------------------------------------------------------------------------------------------------------------------
<S>                                        <C>                          <C>                     <C>                      <C>
Common Stock, 0.01 par
value, reserved for issuance               500,000 Shares               $   13.75(2)            $6,875,000               $2,370.69
pursuant to the 1993
Employee Stock Purchase Plan


          TOTAL                            500,000 Shares               $   13.75               $6,875,000               $2,370.69
                                                                                                                         ---------
</TABLE>



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

(1)   This Registration Statement shall also cover any additional shares of
      Common Stock which become issuable under any of the Plans being registered
      pursuant to this Registration Statement by reason of any stock dividend,
      stock split, recapitalization or any other similar transaction effected
      without the receipt of consideration which results in an increase in the
      number of the Registrant's outstanding shares of Common Stock.

(2)   Computed in accordance with Rule 457(h) under the Securities Act of 1933
      (the "Securities Act") solely for the purpose of calculating the
      registration fee. Computation based on the weighted average high and low
      sale prices of the Common Stock as reported on the Nasdaq National Market
      on February 12, 1997.





                                                                               2
<PAGE>   3
                                   PART II
              INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 3.     INCORPORATION OF DOCUMENTS BY REFERENCE.

      The following documents filed with the Securities and Exchange Commission
(the "Commission") are hereby incorporated by reference:

      (a) The Registrant's Annual Report on Form 10-K for the fiscal year ended
December 31, 1995 filed with the Commission on April 1, 1996 pursuant to Section
13(a) of the Securities Exchange Act of 1934, as amended (the "Exchange Act"),
which contains audited financial statements for the Registrant's latest fiscal
year for which such statements have been filed and as amended by Amendment No. 1
filed on April 5, 1996 and Amendment No. 2 filed on January 14, 1997.

      (b) All other reports filed pursuant to Section 13(a) or 15(d) of the
Exchange Act since the end of the fiscal year covered by the Annual Report
referred to in (a) above.

      (c) The description of the Registrant's Common Stock contained in the
Registrant's Registration Statement on Form 8-A filed with the Commission under
Section 12 of the Exchange Act on January 11, 1993 including any amendment or
report filed for the purpose of updating such description.

      All documents subsequently filed by the Registrant pursuant to Sections
13(a), 13(c), 14 and 15(d) of the Exchange Act, prior to the filing of a
post-effective amendment which indicates that all securities offered hereby have
been sold or which deregisters all securities then remaining unsold, shall be
deemed to be incorporated by reference in this Registration Statement and to be
part hereof from the date of filing such documents.

Item 4.     DESCRIPTION OF SECURITIES.  Not applicable.

Item 5.     INTERESTS OF NAMED EXPERTS AND COUNSEL.  Not applicable.

Item 6.     INDEMNIFICATION OF DIRECTORS AND OFFICERS.

      The Registrant's Certificate of Incorporation reduces the liability of a
director to the corporation or its shareholders for monetary damages for
breaches of his or her fiduciary duty of care to the fullest extent permissible
under Delaware law. The Bylaws of the Registrant further provide for
indemnification of corporate agents to the maximum extent permitted by the
Delaware General Corporation Law. In addition, the Registrant has entered into
Indemnification Agreements with its officers and directors.

Item 7.     EXEMPTION FROM REGISTRATION CLAIMED.  Not applicable.

Item 8.     EXHIBITS.

              Exhibit
              Number
              5.1     Opinion of Venture Law Group, a Professional
                      Corporation.
              23.1    Consent of Venture Law Group, a Professional
                      Corporation (included in Exhibit 5.1).
              23.2    Accountants' Consent
              24.1    Powers of Attorney
              99.1    1993 Employee Stock Purchase Plan


                                                                               3
<PAGE>   4
Item 9.     UNDERTAKINGS.

      The undersigned Registrant hereby undertakes:

            (1)   to file, during any period in which offers or sales are being
made, a post-effective amendment to this registration statement 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.

            (2)   that, for purposes of determining any liability under the
Securities Act, 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.

            (3)   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.

      The undersigned Registrant hereby undertakes that, for purposes of
determining any liability under the Securities Act, each filing of the
Registrant's annual report pursuant to Section 13(a) or Section 15(d) of the
Exchange Act 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.

      Insofar as the indemnification for liabilities arising under the
Securities Act 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 Commission such
indemnification is against public policy as expressed in the Securities 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 a successful defense of any action, suit or proceeding) is asserted by such
director, officer or controlling person in connection with the securities being
registered hereunder, the Registrant will, unless in the opinion of its counsel
the question has already been settled by controlling precedent, submit to a
court of appropriate jurisdiction the question of whether such indemnification
by it is against public policy as expressed in the Securities Act and will be
governed by the final adjudication of such issue.



                           [Signature Pages Follow]

                                                                               4
<PAGE>   5
                                   SIGNATURES


      Pursuant to the requirements of the Securities Act of 1933, the
Registrant, MOLECULAR DYNAMICS, INC., a corporation organized and existing under
the laws of the State of Delaware, 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 Sunnyvale, State of
California, on this 18th day of February, 1997.

                            MOLECULAR DYNAMICS, INC.


                               By:  /s/ Jay Flatley
                                  --------------------------------
                                    Jay Flatley
                                    President, Chief Executive
                                    Officer, Acting Chief
                                    Financial Officer and Director


                                                                               5
<PAGE>   6
                                POWER OF ATTORNEY

      KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature
appears below constitutes and appoints Jay Flatley and Lynne Wagoner, jointly
and severally, his or her attorneys-in-fact and agents, each with the power of
substitution and resubstitution, for him or her and in his or her name, place or
stead, in any and all capacities, to sign any amendments to this Registration
Statement on Form S-8, and to file such amendments, together with exhibits and
other documents in connection therewith, with the Securities and Exchange
Commission, granting to each 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 and about the premises, as fully as he or she might or could do in
person, and ratifying and confirming all that the attorneys-in-fact and agents,
or his or her substitute or substitutes, may 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>
         Signature                      Title                    Date
         ---------                      -----                    ----

<S>                         <C>                            <C>
/s/ Jay Flatley             President and Chief            February 18, 1997
------------------------    Executive Officer, Acting
Jay Flatley                 Chief Financial Officer,
                            and Director (Principal
                            Executive and Financial
                            Officer)
                             
/s/ Lynne Wagoner           Director of Finance            February 18, 1997
------------------------    (Principal Accounting
Lynne Wagoner               Officer)
                             
/s/ James Schlater          Chairman of the Board of       February 18, 1997
------------------------    Directors
James Schlater               

/s/ Robert Keeley           Director                       February 18, 1997
------------------------
Robert Keeley

/s/ Janice M. LeCocq        Director                       February 18, 1997
------------------------
Janice M. LeCocq

/s/ Jack Lloyd              Director                       February 18, 1997
------------------------
Jack Lloyd

/s/ C. Woodrow Rea, Jr.     Director                       February 18, 1997
------------------------
C. Woodrow Rea, Jr.
</TABLE>


                                                                               6
<PAGE>   7
                              INDEX TO EXHIBITS

<TABLE>
<CAPTION>

Exhibit                                                               Page
Number                                                                 No.
------                                                                -----
<S>      <C>                                                          <C>
  5.1    Opinion of Venture Law Group, a Professional Corporation      8

  23.1   Consent of Venture Law Group, a Professional Corporation      8
         (included in Exhibit 5.1).

  23.2   Accountants' Consent                                          9

  24.1   Powers of Attorney                                            6

  99.1   1993 Employee Stock Purchase Plan                             10
</TABLE>



                                                                               7
[{"type": "S-8", "sequence": "1", "description": "FORM S-8", "secsgml_size_bytes": 14866}]
{"company-data": {"conformed-name": "MOLECULAR DYNAMICS INC", "cik": "0000885263", "assigned-sic": "3826", "irs-number": "943050031", "state-of-incorporation": "DE", "fiscal-year-end": "1231"}, "filing-values": {"form-type": "S-8", "act": "33", "file-number": "333-21967", "film-number": "97537623"}, "business-address": {"street1": "928 EAST ARQUES AVE", "city": "SUNNYVALE", "state": "CA", "zip": "94086", "phone": "4087731222"}, "mail-address": {"street2": "928 E ARQUES AVE", "city": "SUNNYVALE", "state": "CA", "zip": "94086"}}
1

                         As filed with the Securities and Exchange Commission on
                                                 Registration No. 333-__________

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549
                                ----------------

                                    FORM S-8

                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933
                                ----------------

                            MOLECULAR DYNAMICS, INC.
             (Exact name of Registrant as specified in its charter)

         DELAWARE                                            94-3050031
 (State of incorporation)                                 (I.R.S. Employer
                                                          Identification No.)

                              928 EAST ARQUES AVE.,
                               SUNNYVALE, CA 94086
                    (Address of principal executive offices)
                             -----------------------

                        1993 EMPLOYEE STOCK PURCHASE PLAN
                            (Full title of the Plan)
                             -----------------------

                                   JAY FLATLEY
                      PRESIDENT AND CHIEF EXECUTIVE OFFICER
                            MOLECULAR DYNAMICS, INC.
                              928 EAST ARQUES AVE.,
                               SUNNYVALE, CA 94086
                                 (408) 733-1222
 (Name, address and telephone number, including area code, of agent for service)
                             -----------------------
                                    Copy to:

                                 Jeffrey Y. Suto
                                Venture Law Group
                               2800 Sand Hill Road
                          Menlo Park, California 94025
                                 (415) 854-4488

                                Page 1 of 9 Pages
                             Exhibit Index on Page 7
               (Calculation of Registration Fee on following page)
2
                       CALCULATION OF REGISTRATION FEE
Proposed                Proposed
                                             Maximum                      Maximum                 Maximum               Amount of
                                            Amount to                    Offering                Aggregate            Registration
   Title of Securities to be                    be                       Price Per               Offering                 Fee
          Registered                       Registered(1)                   Share                   Price
----------------------------------------------------------------------------------------------------------------------------------
Common Stock, 0.01 par
value, reserved for issuance               500,000 Shares               $   13.75(2)            $6,875,000               $2,370.69
pursuant to the 1993
Employee Stock Purchase Plan

          TOTAL                            500,000 Shares               $   13.75               $6,875,000               $2,370.69
                                                                                                                         ---------
-----------------------

(1)   This Registration Statement shall also cover any additional shares of
      Common Stock which become issuable under any of the Plans being registered
      pursuant to this Registration Statement by reason of any stock dividend,
      stock split, recapitalization or any other similar transaction effected
      without the receipt of consideration which results in an increase in the
      number of the Registrant's outstanding shares of Common Stock.

(2)   Computed in accordance with Rule 457(h) under the Securities Act of 1933
      (the "Securities Act") solely for the purpose of calculating the
      registration fee. Computation based on the weighted average high and low
      sale prices of the Common Stock as reported on the Nasdaq National Market
      on February 12, 1997.

                                                                               2
3
                                   PART II
              INFORMATION REQUIRED IN THE REGISTRATION STATEMENT

Item 3.     INCORPORATION OF DOCUMENTS BY REFERENCE.

      The following documents filed with the Securities and Exchange Commission
(the "Commission") are hereby incorporated by reference:

      (a) The Registrant's Annual Report on Form 10-K for the fiscal year ended
December 31, 1995 filed with the Commission on April 1, 1996 pursuant to Section
13(a) of the Securities Exchange Act of 1934, as amended (the "Exchange Act"),
which contains audited financial statements for the Registrant's latest fiscal
year for which such statements have been filed and as amended by Amendment No. 1
filed on April 5, 1996 and Amendment No. 2 filed on January 14, 1997.

      (b) All other reports filed pursuant to Section 13(a) or 15(d) of the
Exchange Act since the end of the fiscal year covered by the Annual Report
referred to in (a) above.

      (c) The description of the Registrant's Common Stock contained in the
Registrant's Registration Statement on Form 8-A filed with the Commission under
Section 12 of the Exchange Act on January 11, 1993 including any amendment or
report filed for the purpose of updating such description.

      All documents subsequently filed by the Registrant pursuant to Sections
13(a), 13(c), 14 and 15(d) of the Exchange Act, prior to the filing of a
post-effective amendment which indicates that all securities offered hereby have
been sold or which deregisters all securities then remaining unsold, shall be
deemed to be incorporated by reference in this Registration Statement and to be
part hereof from the date of filing such documents.

Item 4.     DESCRIPTION OF SECURITIES.  Not applicable.

Item 5.     INTERESTS OF NAMED EXPERTS AND COUNSEL.  Not applicable.

Item 6.     INDEMNIFICATION OF DIRECTORS AND OFFICERS.

      The Registrant's Certificate of Incorporation reduces the liability of a
director to the corporation or its shareholders for monetary damages for
breaches of his or her fiduciary duty of care to the fullest extent permissible
under Delaware law. The Bylaws of the Registrant further provide for
indemnification of corporate agents to the maximum extent permitted by the
Delaware General Corporation Law. In addition, the Registrant has entered into
Indemnification Agreements with its officers and directors.

Item 7.     EXEMPTION FROM REGISTRATION CLAIMED.  Not applicable.

Item 8.     EXHIBITS.

              Exhibit
              Number
              5.1     Opinion of Venture Law Group, a Professional
                      Corporation.
              23.1    Consent of Venture Law Group, a Professional
                      Corporation (included in Exhibit 5.1).
              23.2    Accountants' Consent
              24.1    Powers of Attorney
              99.1    1993 Employee Stock Purchase Plan

                                                                               3
4
Item 9.     UNDERTAKINGS.

      The undersigned Registrant hereby undertakes:

            (1)   to file, during any period in which offers or sales are being
made, a post-effective amendment to this registration statement 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.

            (2)   that, for purposes of determining any liability under the
Securities Act, 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.

            (3)   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.

      The undersigned Registrant hereby undertakes that, for purposes of
determining any liability under the Securities Act, each filing of the
Registrant's annual report pursuant to Section 13(a) or Section 15(d) of the
Exchange Act 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.

      Insofar as the indemnification for liabilities arising under the
Securities Act 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 Commission such
indemnification is against public policy as expressed in the Securities 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 a successful defense of any action, suit or proceeding) is asserted by such
director, officer or controlling person in connection with the securities being
registered hereunder, the Registrant will, unless in the opinion of its counsel
the question has already been settled by controlling precedent, submit to a
court of appropriate jurisdiction the question of whether such indemnification
by it is against public policy as expressed in the Securities Act and will be
governed by the final adjudication of such issue.

                           [Signature Pages Follow]

                                                                               4
5
                                   SIGNATURES

      Pursuant to the requirements of the Securities Act of 1933, the
Registrant, MOLECULAR DYNAMICS, INC., a corporation organized and existing under
the laws of the State of Delaware, 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 Sunnyvale, State of
California, on this 18th day of February, 1997.

                            MOLECULAR DYNAMICS, INC.

                               By:  /s/ Jay Flatley
                                  --------------------------------
                                    Jay Flatley
                                    President, Chief Executive
                                    Officer, Acting Chief
                                    Financial Officer and Director

                                                                               5
6
                                POWER OF ATTORNEY

      KNOW ALL PERSONS BY THESE PRESENTS, that each person whose signature
appears below constitutes and appoints Jay Flatley and Lynne Wagoner, jointly
and severally, his or her attorneys-in-fact and agents, each with the power of
substitution and resubstitution, for him or her and in his or her name, place or
stead, in any and all capacities, to sign any amendments to this Registration
Statement on Form S-8, and to file such amendments, together with exhibits and
other documents in connection therewith, with the Securities and Exchange
Commission, granting to each 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 and about the premises, as fully as he or she might or could do in
person, and ratifying and confirming all that the attorneys-in-fact and agents,
or his or her substitute or substitutes, may 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/ Jay Flatley             President and Chief            February 18, 1997
------------------------    Executive Officer, Acting
Jay Flatley                 Chief Financial Officer,
                            and Director (Principal
                            Executive and Financial
                            Officer)
                             
/s/ Lynne Wagoner           Director of Finance            February 18, 1997
------------------------    (Principal Accounting
Lynne Wagoner               Officer)
                             
/s/ James Schlater          Chairman of the Board of       February 18, 1997
------------------------    Directors
James Schlater               

/s/ Robert Keeley           Director                       February 18, 1997
------------------------
Robert Keeley

/s/ Janice M. LeCocq        Director                       February 18, 1997
------------------------
Janice M. LeCocq

/s/ Jack Lloyd              Director                       February 18, 1997
------------------------
Jack Lloyd

/s/ C. Woodrow Rea, Jr.     Director                       February 18, 1997
------------------------
C. Woodrow Rea, Jr.
6
7
                              INDEX TO EXHIBITS
Exhibit                                                               Page
Number                                                                 No.
------                                                                -----
5.1    Opinion of Venture Law Group, a Professional Corporation      8

  23.1   Consent of Venture Law Group, a Professional Corporation      8
         (included in Exhibit 5.1).

  23.2   Accountants' Consent                                          9

  24.1   Powers of Attorney                                            6

  99.1   1993 Employee Stock Purchase Plan                             10
7