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                                                                     EXHIBIT 3.1


                            CERTIFICATE OF AMENDMENT

                                       OF
                              AMENDED AND RESTATED
                          CERTIFICATE OF INCORPORATION
                                       OF
                         KOSAN BIOSCIENCES INCORPORATED


        KOSAN BIOSCIENCES INCORPORATED, a corporation organized and existing
under the General Corporation Law of the State of Delaware, does hereby certify
as follows:

        FIRST: The name of the corporation is KOSAN BIOSCIENCES INCORPORATED.

        SECOND: The original Certificate of Incorporation of the corporation was
filed with the Secretary of State of the State of Delaware on April 6, 2000. An
amendment to the Certificate of Incorporation was filed with the Delaware
Secretary of State on September 27, 2000. An Amended and Restated Certificate of
Incorporation was filed with the Secretary of State of the State of Delaware on
October 10, 2000.

        THIRD: The following amendment to the Certificate of Incorporation was
duly adopted in accordance with the provisions of Section 242 of the General
Corporation Law of the State of Delaware (the "General Corporation Law") by
resolutions duly adopted by the Board of Directors of this Corporation and was
approved by the stockholders as provided in Section 228 of the General
Corporation Law.

        FOURTH: The first paragraph of Article Fourth of the Amended and
Restated Certificate of Incorporation is hereby deleted in its entirety and
replaced with the following:

                "1. The Corporation is authorized to issue 100,000,000 shares of
        Common Stock, par value $0.001 per share (the "Common Stock"), and
        10,000,000 shares of Preferred Stock, par value $0.001 per share (the
        "Preferred Stock")."



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        IN WITNESS WHEREOF, KOSAN BIOSCIENCES INCORPORATED has caused this
Certificate of Amendment of Amended and Restated Certificate of Incorporation to
be signed by its Chief Executive Officer and Secretary in Hayward, California
this 18th day of July, 2001.

                                            KOSAN BIOSCIENCES INCORPORATED


                                            /s/  Daniel V. Santi
                                            ------------------------------------
                                            Daniel V. Santi, M.D., Ph.D.
                                            Chief Executive Officer


Attest:

/s/ Susan Kanaya
---------------------------------------
Susan Kanaya
Chief Financial Officer and Secretary



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                AMENDED AND RESTATED CERTIFICATE OF INCORPORATION
                                       OF
                         KOSAN BIOSCIENCES INCORPORATED
                             A DELAWARE CORPORATION

Daniel V. Santi and Blair W. Stewart hereby certify that:

        1. They are the President and Secretary, respectively, of Kosan
Biosciences Incorporated, a Delaware Corporation (the "Corporation").

        2. The Certificate of Incorporation of the Corporation, filed with the
Secretary of State of the State of Delaware on April 6, 2000, as amended on
September 27, 2000, is hereby amended and restated in its entirety to read as
follows:

        FIRST: The name of the corporation is Kosan Biosciences Incorporated
(the "Corporation").

        SECOND: The address of the Corporation's registered office in the State
of Delaware is Corporation Trust Center, 1209 Orange Street, in the City of
Wilmington, County of New Castle, Delaware, 19801. The name of its registered
agent at such address is The Corporation Trust Company.

        THIRD: The nature of the business or purposes to be conducted or
promoted by the Corporation is to engage in any lawful act or activity for which
corporations may be organized under the General Corporation Law of Delaware.

        FOURTH: This Corporation is authorized to issue two classes of shares
designated Common Stock and Preferred Stock.

        1. The Corporation is authorized to issue 200,000,000 shares of Common
Stock, par value $0.001 per share (the "Common Stock"), and 10,000,000 shares of
Preferred Stock, par value $0.001 per share (the "Preferred Stock").

        2. The shares of Preferred Stock may be issued from time to time in one
or more series pursuant to a resolution or resolutions providing for such issue
duly adopted by the Board of Directors. The Board of Directors of the
Corporation is expressly authorized, by filing a certificate pursuant to the
applicable law of the State of Delaware, to: (i) establish from time to time the
number of shares to be included in each such series; (ii) fix the rights,
preferences, restrictions and designations of the shares of each such series,
including but not limited to the fixing or alteration of the dividend rights,
dividend rate, conversion rights, conversion rate, voting rights, rights and
terms of redemption (including sinking fund provisions), redemption price or
prices, voting rights and liquidation preferences of any series of Preferred
Stock for which no shares have been issued and are outstanding; (iii) increase
number of shares of any series at any time; and (iv) decrease the number of
shares of any series prior or subsequent to the issue of shares of that series,
but not below the number of shares of such series then outstanding. In case the
number of shares of any series shall be so decreased, the shares constituting
such decrease shall resume the status which they had prior to the adoption of
the resolution originally fixing the number of shares of such series.

        FIFTH: In furtherance and not in limitation of the powers conferred by
statute, the Board of Directors is expressly authorized to make, alter, amend,
or repeal the Bylaws of the Corporation.

        SIXTH: Advance notice of new business and stockholder nominations for
the election of directors shall be given in the manner and to the extent
provided in the Bylaws of the Corporation. Election of directors need not be by
written ballot unless the Bylaws of the Corporation shall so provide.

        SEVENTH: Meetings of stockholders may be held within or without the
State of Delaware, as the Bylaws may provide. No action that is required or
permitted to be taken by the stockholders of the Corporation at any annual or
special meeting of stockholders may be effected by written consent of
stockholders in lieu of a meeting of stockholders. The books of the Corporation
may be kept (subject to any provision contained in the statutes) outside of the
State of Delaware at such place or places as may be



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designated from time to time by the Board of Directors or in the Bylaws of the
Corporation. The directors of the Corporation need not be elected by written
ballot unless a stockholder demands election by written ballot at the meeting
and before voting begins, or unless the Bylaws so provide.

        EIGHTH: The Corporation reserves the right to amend, alter, change or
repeal any provision contained in this Certificate of Incorporation, in the
manner now or hereafter prescribed by statute, and all rights conferred upon the
stockholders herein are granted subject to this right.

        NINTH: Subject to the provisions of the General Corporation Law of the
State of Delaware, the number of Directors of the Corporation shall be
determined as provided by the Bylaws.

        TENTH: The Board of Directors shall be divided into three classes
consisting of as nearly equal numbers of directors as possible, and designated
Class A, Class B, and Class C. The term of office of Class A shall expire at the
first annual meeting of stockholders following the effectiveness of this
Article, and each third annual meeting of stockholders thereafter; the term of
office of Class B shall expire at the second annual meeting of stockholders
following the effectiveness of this Article, and each third annual meeting of
stockholders thereafter; and the term of office of Class C shall expire at the
third annual meeting of stockholders following the effectiveness of this
Article, and each third annual meeting of stockholders thereafter. Directors
added to the board of directors between annual meetings of stockholders by
reason of an increase in the authorized number of directors shall belong to the
class designated by the Board of Directors; provided however that the number of
board seats designated to belong to Class A, Class B and Class C must be as
nearly equal in number as possible. Following the effectiveness of this Article,
stockholders may effect the removal of a director only for cause. This provision
shall supersede any provision to the contrary in the Corporation's Bylaws.

        ELEVENTH: The Corporation shall indemnify and hold harmless any
director, officer, employee or agent of the Corporation from and against any and
all expenses and liabilities that may be imposed upon or incurred by him in
connection with, or as a result of, any proceeding in which he may become
involved, as a part or otherwise, by reason of the fact that he is or was such a
director, officer, employee or agent of the Corporation, whether or not he
continues to be such at the time such expenses and liabilities shall have been
imposed or incurred, to the extent permitted by the laws of the State of
Delaware, as they may be amended from time to time.

        TWELFTH: The liability of the directors of the Corporation for monetary
damages shall be eliminated to the fullest extent permissible under Delaware
law.

        A director of the Corporation shall not be personally liable to the
Corporation or its stockholders for monetary damages for any breach of fiduciary
duty as a director, except for liability (i) for any breach of the director's
duty of loyalty to the Corporation or its stockholders, (ii) for acts or
omissions not in good faith or which involve intentional misconduct or a knowing
violation of law, (iii) under Section 174 of the Delaware General Corporation
Law, or (iv) for any transaction from which the director derived an improper
personal benefit. If the Delaware General Corporation Law is amended after
approval by the stockholders of this Article to authorize corporate action
further eliminating or limiting the personal liability of directors, then the
liability of a director shall be eliminated or limited to the fullest extent
permitted by the Delaware General Corporation Law, as so amended.

        Any repeal or modification of this TWELFTH Article shall be prospective
and shall not affect the rights under this TWELFTH Article in effect at the time
of the alleged occurrence of any act or omission to act giving rise to liability
or indemnification.

        3. The foregoing Restated Certificate of Incorporation has been duly
approved by the board of directors of the Corporation in accordance with the
provisions of Sections 242 and 245 of the Delaware General Corporation Law.



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        4. The foregoing Restated Certificate of Incorporation has been duly
approved by the required vote of the stockholders in accordance with the
Certificate of Incorporation and the provisions of Sections 242 and 245 of the
Delaware General Corporation Law.

        The undersigned hereby acknowledges that the foregoing Restated
Certificate of Incorporation is his act and deed and that the facts stated
herein are true.

           Executed at Palo Alto, CA, this 10th day of October, 2000.

/s/ Daniel V. Santi                      /s/ Blair W. Stewart
------------------------------------     ---------------------------------------
Daniel V. Santi, President               Blair W. Stewart, Secretary



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