Exhibit 99.1

CERTIFICATION

Pursuant to Section 906 of the Public Company Accounting Reform Investor and Protection Act of 2002 (18 U.S.C. § 1350, as adopted) (the “Sarbanes-Oxley Act of 2002”), Daniel V. Santi, M.D., Ph.D., the Chief Executive Officer of Kosan Biosciences Incorporated, a Delaware corporation (the “Company”), and Susan M. Kanaya, the Chief Financial Officer of the Company, each hereby certifies that, to his or her knowledge:

(a) The Company’s Quarterly Report on Form 10-Q for the period ended June 30, 2002, to which this Certification is attached as Exhibit 99.1 (the “Periodic Report”), fully complies with the requirements of section 13(a) or section 15(d) of the Securities Exchange Act of 1934, as amended; and

(b) The information contained in the Periodic Report fairly presents, in all material respects, the financial condition of the Company at the end of the periods covered by the Periodic Report and the results of operations of the Company for the periods covered by the Periodic Report.

This certification accompanies the Periodic Report pursuant to §906 of the Sarbanes-Oxley Act of 2002 and shall not be deemed “filed” by the Company for purposes of Section 18 of the Securities Exchange Act of 1934, as amended.

Dated: August 13, 2002

/s/    DANIEL V. SANTI, M.D., PH.D.

Daniel V. Santi, M.D., Ph.D.

Chief Executive Officer

/s/    SUSAN M. KANAYA

Susan M. Kanaya

Chief Financial Officer