Exhibit



                                                                                                                                Exhibit 10.1
Codexis, Inc.
 
200 Penobscot Drive
 
Redwood City, CA  94063
 
Tel:  +1 650.421.8100
 
Fax: +1 650.421.8102
 
www.codexis.com 





March 21, 2016


James Lalonde
615 Georgia Avenue
Palo Alto, CA 94306


Re:     Amendment to Change of Control Severance Agreement
Dear Jim,
You and Codexis, Inc. (the “Company”) are currently parties to a Change of Control Severance Agreement, dated as of February 28, 2014 (the “CoC Agreement”), which provides that you will be entitled to receive certain severance payments and benefits upon certain qualifying terminations of employment.  Effective as of the date of this amendment (this “Amendment”), you and the Company hereby agree to amend the CoC Agreement as follows:
1.The following provision is hereby added to the end of Section 3(b) of CoC Agreement:
“Notwithstanding the foregoing, any outstanding performance stock units held by Executive shall automatically become vested with respect to: (i) in the event of a Change of Control that occurs prior to the applicable Measurement Date, such number of shares of Company common stock corresponding to the target performance level for any applicable performance goals; or (ii) in the event of a Change of Control that occurs on or after the Measurement Date, such number of shares of Company common stock corresponding to the Company’s actual achievement of any applicable performance  goals.”
2.    The following provision is hereby added to the end of Section 4(a) of CoC Agreement: 
“For purposes of determining the number of shares subject to any outstanding performance stock units that would otherwise vest on the next vesting date pursuant to the foregoing sentence, the applicable performance goals shall be deemed achieved: (i) in the event of a Change of Control that occurs prior to the applicable Measurement Date, at the target performance level; or (ii) in the event of a Change of Control that occurs on or after the Measurement Date, based on the Company’s actual achievement.”
3.     The following definition is added as a new Section 8(f):
“Measurement Date.  ‘Measurement Date’, with respect to an award of performance stock units, shall mean the date the Compensation Committee of the Board of Directors determines the final performance factor for the applicable performance period.”
All terms and provisions of the CoC Agreement not amended hereby, either expressly or by necessary implication, shall remain in full force and effect.  From and after the date of this Amendment, all references 


Codexis, Inc.   200 Penobscot Drive   Redwood City, CA  94063   Tel:  650.421.8100    www.codexis.com









to the term “CoC Agreement” in this Amendment or the original CoC Agreement shall include the terms contained in this Amendment.
Please indicate your acceptance of and agreement to the terms and conditions set forth in this Amendment by signing in the space below and returning the executed Amendment to the Company.  
                            
Sincerely,


Codexis, Inc.






By:        /s/ John Nicols                


Name:    John Nicols


Title:    President and Chief Executive                                     Officer


Accepted by:






/s/ James Lalonde                
James Lalonde




March 21, 2016                
Date








Codexis, Inc.   200 Penobscot Drive   Redwood City, CA  94063   Tel:  650.421.8100    www.codexis.com