April 5, 2010     VIA EDGAR AND HAND DELIVERY   United States Securities and Exchange Commission Division of Corporation Finance 100 F Street, N.E., Mail Stop 4631 Washington, D.C. 20549-6010

Dear Ms. Long:

On behalf of Codexis, Inc. (the “Company”), we are hereby filing Amendment No. 7 (“Amendment No. 7”) to the Company’s above-referenced Registration Statement on Form S-1, which was initially filed with the Securities and Exchange Commission (the “Commission”) on December 28, 2009 (the “Initial Form S-1”), and amended by Amendment No. 1 on January 14, 2010, Amendment No. 2 on February 1, 2010, Amendment No. 3 on February 17, 2010, Amendment No. 4 on February 26, 2010, Amendment No. 5 on March 26, 2010 and Amendment No. 6 on March 31, 2010 (as amended, the “Registration Statement”). For your convenience, we have enclosed a courtesy package which includes five copies of Amendment No. 7, three of which have been marked to show changes from Amendment No. 6.

April 5, 2010

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Amendment No. 7 has been revised to reflect the Company’s responses to oral comments from the staff of the Commission (the “Staff”) received by the undersigned and Mr. Gregory Chin on April 2, 2010. For ease of review, we have set forth below each of the numbered comments of your discussion and the Company’s responses thereto.

Management’s Discussion and Analysis of Financial Condition and Results of Operations

Critical Accounting Policies and Estimates

Stock-based Compensation, page 55

Response: In response to the Staff’s comments, the Company respectfully advises the Staff that it has revised its disclosure in Amendment No. 7 to disclose that, at December 31, 2009, there was $13.7 million of unrecognized stock-based compensation cost, which is expected to be recognized over an average period of 2.8 years.

Part II – Information Not Required in Prospectus, page II-1

Item 16. Exhibits and Financial Statement Schedules, page II-3

Response: In response to the Staff’s comment, we hereby confirm that the legality opinion concurs with the Staff’s understanding that the reference and limitation to the Delaware General Corporation Law in our opinion dated March 31, 2010 provided to the Company and filed as Exhibit 5.1 to the Registration Statement includes the statutory provisions and also all applicable provisions of the Delaware Constitution and the reported judicial cases interpreting those laws currently in effect.

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April 5, 2010

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We hope the foregoing answers are responsive to your comments. Please do not hesitate to contact me by telephone at (650) 463-3067 or by fax at (650) 463-2600 with any questions or comments regarding this correspondence.