<SEC-DOCUMENT>0001140361-11-030888.txt : 20110602
<SEC-HEADER>0001140361-11-030888.hdr.sgml : 20110602
<ACCEPTANCE-DATETIME>20110602092028
ACCESSION NUMBER:		0001140361-11-030888
CONFORMED SUBMISSION TYPE:	3
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:			Ispagnac Participacoes Ltda.
		CENTRAL INDEX KEY:			0001517347

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		11887196

	BUSINESS ADDRESS:	
		STREET 1:		FUNCHAL ST, 418-11 FLOOR-ROOM H 11
		CITY:			VILA OLIMPIA, SAO PAULO
		STATE:			D5
		ZIP:			04 551 060
		BUSINESS PHONE:		5521-3984-8970

	MAIL ADDRESS:	
		STREET 1:		FUNCHAL ST, 418-11 FLOOR-ROOM H 11
		CITY:			VILA OLIMPIA, SAO PAULO
		STATE:			D5
		ZIP:			04 551 060
</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>2011-05-31</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001517347</rptOwnerCik>
            <rptOwnerName>Ispagnac Participacoes Ltda.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>AVENIDA DAS AMERICAS, 4200 BLOCO 6,</rptOwnerStreet1>
            <rptOwnerStreet2>1O ANDAR, (PART) BARRA DA TIJUCA</rptOwnerStreet2>
            <rptOwnerCity>RIO DE JANEIRO, RJ CEP</rptOwnerCity>
            <rptOwnerState>D5</rptOwnerState>
            <rptOwnerZipCode>22640-102</rptOwnerZipCode>
            <rptOwnerStateDescription>BRAZIL</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 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/ Matias Lopes for Ispagnac Participacoes Ltda as an Officer</signatureName>
        <signatureDate>2011-05-31</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
