<SEC-DOCUMENT>0001140361-11-029470.txt : 20110524
<SEC-HEADER>0001140361-11-029470.hdr.sgml : 20110524
<ACCEPTANCE-DATETIME>20110524112123
ACCESSION NUMBER:		0001140361-11-029470
CONFORMED SUBMISSION TYPE:	3
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20110520
FILED AS OF DATE:		20110524
DATE AS OF CHANGE:		20110524

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			CODEXIS INC
		CENTRAL INDEX KEY:			0001200375
		STANDARD INDUSTRIAL CLASSIFICATION:	INDUSTRIAL ORGANIC CHEMICALS [2860]
		IRS NUMBER:				710872999

	BUSINESS ADDRESS:	
		STREET 1:		200 PENOBSCOT DRIVE
		CITY:			REDWOOD CITY
		STATE:			CA
		ZIP:			94063
		BUSINESS PHONE:		650-421-8100

	MAIL ADDRESS:	
		STREET 1:		200 PENOBSCOT DRIVE
		CITY:			REDWOOD CITY
		STATE:			CA
		ZIP:			94063

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Shell Brazil Holding B.V.
		CENTRAL INDEX KEY:			0001517349

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		11867204

	BUSINESS ADDRESS:	
		STREET 1:		P.O. BOX 162
		CITY:			THE HAGUE
		STATE:			P7
		ZIP:			2501 AN
		BUSINESS PHONE:		31-70-377-9111

	MAIL ADDRESS:	
		STREET 1:		P.O. BOX 162
		CITY:			THE HAGUE
		STATE:			P7
		ZIP:			2501 AN
</SEC-HEADER>
<DOCUMENT>
<TYPE>3
<SEQUENCE>1
<FILENAME>doc1.xml
<DESCRIPTION>FORM 3
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0203</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2011-05-20</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001200375</issuerCik>
        <issuerName>CODEXIS INC</issuerName>
        <issuerTradingSymbol>CDXS</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001517349</rptOwnerCik>
            <rptOwnerName>Shell Brazil Holding B.V.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>P.O. BOX 162</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>THE HAGUE</rptOwnerCity>
            <rptOwnerState>P7</rptOwnerState>
            <rptOwnerZipCode>2501 AN</rptOwnerZipCode>
            <rptOwnerStateDescription>NETHERLANDS</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>5573319</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable></derivativeTable>

    <footnotes>
        <footnote id="F1">Acquisition of Codexis Common Stock was effected via transfer of such Common Stock from Equilon Enterprises LLC, an indirect wholly owned subsidiary of Royal Dutch Shell plc (&quot;RDS&quot;), to Shell Brazil Holding B.V., an indirect wholly owned subsidiary of Royal Dutch Shell plc for $10.07 per share, the closing price for shares of Codexis Common Stock on 5/20/11.  RDS's beneficial ownership of the Codexis Common Stock was not affected by the transfer.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Stephen Rees, for Shell Brazil Holding B.V. as its Director</signatureName>
        <signatureDate>2011-05-20</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
