<PAGE>

As filed with the Securities and Exchange Commission on September 5, 1997
                                             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                                 94-3090031
 (State of incorporation)             (I.R.S. Employer Identification No.)

                          928 EAST ARQUES AVENUE
                           SUNNYVALE, CA 94086
                  (Address of principal executive offices)
                         _______________________

                     RESTATED 1997 STOCK OPTION PLAN
                         (Full title of the Plan)
                         _______________________

                               JAY FLATLEY
                         CHIEF EXECUTIVE OFFICER
                         MOLECULAR DYNAMICS, INC.
                          928 EAST ARQUES AVENUE
                           SUNNYVALE, CA 94086
                              (408) 773-1222
(Name, address and telephone number, including area code, of agent for service)
                         _______________________
                                Copy to:
                            Jeffrey Y. Suto
                           Venture Law Group
                       A Professional Corporation
                          2800 Sand Hill Road
                      Menlo Park, California 94025
                             (650) 854-4488

                          Page 1 of 31 Pages
                        Exhibit Index on Page 7
           (Calculation of Registration Fee on following page)


<PAGE>

<TABLE>
<CAPTION>
- -----------------------------------------------------------------------------------------------------------------
                                 CALCULATION OF REGISTRATION FEE
- -----------------------------------------------------------------------------------------------------------------

                                                               Proposed          Proposed        
                                               Maximum          Maximum           Maximum            Amount of
                                             Amount to be    Offering Price      Aggregate         Registration
Title of Securities to be Registered         Registered(1)     Per Share       Offering Price           Fee
- -----------------------------------------------------------------------------------------------------------------
<S>                                         <C>              <C>               <C>                 <C>
Common Stock issuable upon exercise of 
options granted pursuant to the Restated    500,000 Shares   $  22.69(2)(3)   $  11,345,000.00       $3,437.88
1997 Stock Option Plan
$0.01 par value

Options to purchase Common Stock 
(under Restated 1997 Stock Option Plan)     500,000 Shares       $  n/a           $  n/a              $  n/a
$0.01 par value
    
       TOTAL                                500,000 Shares   $  22.69         $  11,345,000.00       $3,437.88

</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 per share
     exercise price (rounded to nearest cent) of outstanding options under the
     referenced plan, the shares issuable under which are registered hereby.

(3)  Estimated in accordance with Rule 457(h) under the Securities Act solely
     for the purpose of calculating the registration fee.  The computation with
     respect to unissued options is based upon the average high and low sale
     prices of the Common Stock as reported on the Nasdaq National Market on
     September 4, 1997.


                                      -2-
<PAGE>

                                    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, 1996 filed 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.

     (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   Consent of Independent Auditors.
           24.1   Powers of Attorney.
           99.1   Restated 1997 Stock Option Plan

_______________



                                  -3-

<PAGE>

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>

                                 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 5th day of September, 1997.

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



                                    -5-

<PAGE>

                              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 attorney-in-facts 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>
<CAPTION>

   Signature                               Title                             Date
   ---------                               -----                             ----
<S>                         <C>                                        <C>
/s/ Jay Flatley             President, Chief Executive Officer,        September 5, 1997
- -------------------------    Acting Chief Financial Officer and
Jay Flatley                  Director (Principal Executive Officer)


/s/ Lynne Wagoner     
- -------------------------   Director of Finance (Principal             September 5, 1997
Lynne Wagoner                Accounting Officer)

/s/ James Schlater    
- -------------------------   Chairman of the Board of                   September 5, 1997
James Schlater               Directors

/s/ Robert Keeley     
- -------------------------   Director                                   September 5, 1997
Robert Keeley        

/s/ Janice M. LeCocq  
- -------------------------   Director                                   September 5, 1997
Janice M. LeCocq

/s/ Jack Lloyd        
- -------------------------   Director                                   September 5, 1997
Jack Lloyd 

/s/ C. Woodrow Rea, Jr.
- -------------------------   Director                                   September 5, 1997
C. Woodrow Rea, Jr.
</TABLE>


                                    -5-

<PAGE>


                             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      Consent of Independent Auditors                               9

24.1      Powers of Attorney (see page number)                          6

99.1      Restated 1997 Stock Option Plan                              10
[{"type": "S-8", "sequence": "1", "description": "S-8", "secsgml_size_bytes": 14766}]
{"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", "file-number": "333-35145", "film-number": "97676821"}, "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"}}
As filed with the Securities and Exchange Commission on September 5, 1997
                                             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                                 94-3090031
 (State of incorporation)             (I.R.S. Employer Identification No.)

                          928 EAST ARQUES AVENUE
                           SUNNYVALE, CA 94086
                  (Address of principal executive offices)
                         _______________________

                     RESTATED 1997 STOCK OPTION PLAN
                         (Full title of the Plan)
                         _______________________

                               JAY FLATLEY
                         CHIEF EXECUTIVE OFFICER
                         MOLECULAR DYNAMICS, INC.
                          928 EAST ARQUES AVENUE
                           SUNNYVALE, CA 94086
                              (408) 773-1222
(Name, address and telephone number, including area code, of agent for service)
                         _______________________
                                Copy to:
                            Jeffrey Y. Suto
                           Venture Law Group
                       A Professional Corporation
                          2800 Sand Hill Road
                      Menlo Park, California 94025
                             (650) 854-4488

                          Page 1 of 31 Pages
                        Exhibit Index on Page 7
           (Calculation of Registration Fee on following page)
- -----------------------------------------------------------------------------------------------------------------
                                 CALCULATION OF REGISTRATION FEE
- -----------------------------------------------------------------------------------------------------------------

                                                               Proposed          Proposed        
                                               Maximum          Maximum           Maximum            Amount of
                                             Amount to be    Offering Price      Aggregate         Registration
Title of Securities to be Registered         Registered(1)     Per Share       Offering Price           Fee
- -----------------------------------------------------------------------------------------------------------------
Common Stock issuable upon exercise of 
options granted pursuant to the Restated    500,000 Shares   $  22.69(2)(3)   $  11,345,000.00       $3,437.88
1997 Stock Option Plan
$0.01 par value

Options to purchase Common Stock 
(under Restated 1997 Stock Option Plan)     500,000 Shares       $  n/a           $  n/a              $  n/a
$0.01 par value
    
       TOTAL                                500,000 Shares   $  22.69         $  11,345,000.00       $3,437.88
_______________________
(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 per share
     exercise price (rounded to nearest cent) of outstanding options under the
     referenced plan, the shares issuable under which are registered hereby.

(3)  Estimated in accordance with Rule 457(h) under the Securities Act solely
     for the purpose of calculating the registration fee.  The computation with
     respect to unissued options is based upon the average high and low sale
     prices of the Common Stock as reported on the Nasdaq National Market on
     September 4, 1997.

                                      -2-
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, 1996 filed 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.

     (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   Consent of Independent Auditors.
           24.1   Powers of Attorney.
           99.1   Restated 1997 Stock Option Plan

_______________

                                  -3-
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-
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 5th day of September, 1997.

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

                                    -5-
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 attorney-in-facts 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, Chief Executive Officer,        September 5, 1997
- -------------------------    Acting Chief Financial Officer and
Jay Flatley                  Director (Principal Executive Officer)

/s/ Lynne Wagoner     
- -------------------------   Director of Finance (Principal             September 5, 1997
Lynne Wagoner                Accounting Officer)

/s/ James Schlater    
- -------------------------   Chairman of the Board of                   September 5, 1997
James Schlater               Directors

/s/ Robert Keeley     
- -------------------------   Director                                   September 5, 1997
Robert Keeley        

/s/ Janice M. LeCocq  
- -------------------------   Director                                   September 5, 1997
Janice M. LeCocq

/s/ Jack Lloyd        
- -------------------------   Director                                   September 5, 1997
Jack Lloyd 

/s/ C. Woodrow Rea, Jr.
- -------------------------   Director                                   September 5, 1997
C. Woodrow Rea, Jr.
-5-
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      Consent of Independent Auditors                               9

24.1      Powers of Attorney (see page number)                          6

99.1      Restated 1997 Stock Option Plan                              10