Exhibit 4.1

PFEnex(Exhibit 4.1CUSIP 717D71 ID 4

SEE REVERSE FOR CERTAIN DEFINITIONS DELAWARE

This certifies that is the record holder of

FULLY PAID AND NONASSESSABLE SHARES OF COMMON STOCK, $0,001 PAR VALUE, OF

PFENEX INC.

transferable on the books of the corporation in person or by duly authorized attorney upon surrender of this Certificate properly endorsed. This Certificate is not valid until countersigned by the Transfer Agent and registered by the Registrar.

WITNESS the facsimile seal of the Corporation and the facsimile signatures of its duly authorized officers.

Dated:

# %

PRESIDENT & CHIEF EXECUTIVE OFFICER S / gEAL \ = SECRETARY

The Corporation shall furnish without charge to each stockholder who so requests a statement of the powers, designations, preferences and relative, participating, optional or other special rights of each class of stock of the Corporation or series thereof and the qualifications, limitations or restrictions of such preferences and/or rights. Such requests shall be made to the Corporation s Secretary at the principal office of the Corporation.

The following abbreviations, when used in the inscription on the face of this certificate, shall be construed as though they were written out in full according to applicable laws or regulations:

UNIF GIFT MIN ACT - Custodian

TEN COM - as tenants in common UfNir ^’r ‘ (Cugt) (Minor)

TEN ENT - as tenants by the entireties under Uniform Gjfts lQ Mjnors

JT TEN - as joint tenants with right of Act

survivorship and not as tenants (State)

in common UNIF ACT _ Custodian (until age )

COM PROP - as community property (Cust)

under Uniform Transfers

(Minor)

to Minors Act

(State)

Additional abbreviations may also be used though not in the above list.

FOR VALUE RECEIVED - hereby sel|(s>’ assi9”<s) and tra”Sfer(S) Unt°

PLEASE INSERT SOCIAL SECURITY OR OTHER IDENTIFYING NUMBER OF ASSIGNEE

(PLEASE PRINT OR TYPEWRITE NAME AND ADDRESS, INCLUDING ZIP CODE, OF ASSIGNEE)

shares

of the capital stock represented by within Certificate, and do hereby irrevocably constitute and appoint

attorney-in-fact

to transfer the said stock on the books of the within named Corporation with full power of the substitution in the premises.

Dated —

X

X

NOTICF- THE SIGNATURE TO THIS ASSIGNMENT MUST CORRESPOND WITH THE NAME AS VVR|TTEN UPON “mE

Signature(s) Guaranteed:

NOTICE. ™ EvERY PARTICULAR. WITHOUT ALTERATION OR ENLARGEMENT OR ANY

By

PU^a^TO S.EC. RULE ITAd-15. GUARANTEES BYANOTARY PUBLIC ARE NOT ACCEPTABLE. SIGNATURE GUARANTEES MUST NOT BE DATED.