<SEC-DOCUMENT>0001140361-11-030887.txt : 20110602
<SEC-HEADER>0001140361-11-030887.hdr.sgml : 20110602
<ACCEPTANCE-DATETIME>20110602091913
ACCESSION NUMBER:		0001140361-11-030887
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20110531
FILED AS OF DATE:		20110602
DATE AS OF CHANGE:		20110602

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:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		11887195

	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>4
<SEQUENCE>1
<FILENAME>doc1.xml
<DESCRIPTION>FORM 4
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2011-05-31</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <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>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2011-05-31</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>5573319</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>5573319</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable></derivativeTable>

    <footnotes>
        <footnote id="F1">Disposition of Codexis Common Stock was effected via a transfer of such Common Stock from Shell Brazil Holding B.V., an indirect wholly owned subsidiary of Royal Dutch Shell plc (&quot;RDS&quot;), to Ispagnac Participacoes Ltda., an indirect wholly owned subsidiary of Royal Dutch Shell plc in exchange for capital stock of Ispagnac Participacoes Ltda.  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>2011-05-31</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
