<SEC-DOCUMENT>0001140361-11-031228.txt : 20110603
<SEC-HEADER>0001140361-11-031228.hdr.sgml : 20110603
<ACCEPTANCE-DATETIME>20110603144315
ACCESSION NUMBER:		0001140361-11-031228
CONFORMED SUBMISSION TYPE:	3
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20110601
FILED AS OF DATE:		20110603
DATE AS OF CHANGE:		20110603

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:			Royal Dutch Shell plc
		CENTRAL INDEX KEY:			0001306965
		STANDARD INDUSTRIAL CLASSIFICATION:	CRUDE PETROLEUM & NATURAL GAS [1311]
		STATE OF INCORPORATION:			X0
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		11891742

	BUSINESS ADDRESS:	
		STREET 1:		CAREL VAN BYLANDTLAAN 30
		CITY:			THE HAGUE
		STATE:			P7
		ZIP:			2596 HR
		BUSINESS PHONE:		31-70-377-9111

	MAIL ADDRESS:	
		STREET 1:		CAREL VAN BYLANDTLAAN 30
		CITY:			THE HAGUE
		STATE:			P7
		ZIP:			2596 HR

	FORMER NAME:	
		FORMER CONFORMED NAME:	Forthdeal LTD
		DATE OF NAME CHANGE:	20041026

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Cosan Ltd.
		CENTRAL INDEX KEY:			0001402902
		STANDARD INDUSTRIAL CLASSIFICATION:	SUGAR & CONFECTIONERY PRODUCTS [2060]
		STATE OF INCORPORATION:			D0
		FISCAL YEAR END:			0430

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		11891740

	BUSINESS ADDRESS:	
		STREET 1:		AV. PRESIDENTE JUSCELINO KUBITSCHEK
		STREET 2:		1726, 6TH FLOOR
		CITY:			SAO PAULO, SP
		STATE:			D5
		ZIP:			04543-000
		BUSINESS PHONE:		55-11-3897-9797

	MAIL ADDRESS:	
		STREET 1:		AV. PRESIDENTE JUSCELINO KUBITSCHEK
		STREET 2:		1726, 6TH FLOOR
		CITY:			SAO PAULO, SP
		STATE:			D5
		ZIP:			04543-000

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Cosan S.A. Industria e Comercio
		CENTRAL INDEX KEY:			0001430162
		STATE OF INCORPORATION:			D5
		FISCAL YEAR END:			0430

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		11891741

	BUSINESS ADDRESS:	
		STREET 1:		AV. JUSCELINO KUBITSCHEK
		STREET 2:		1726 - 6TH FLOOR
		CITY:			SAO PAUO, SP
		STATE:			D5
		ZIP:			04543-000
		BUSINESS PHONE:		55-11-3897-9797

	MAIL ADDRESS:	
		STREET 1:		AV. JUSCELINO KUBITSCHEK
		STREET 2:		1726 - 6TH FLOOR
		CITY:			SAO PAUO, SP
		STATE:			D5
		ZIP:			04543-000

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:		11891743

	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

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Raizen Energia Participacoes S.A.
		CENTRAL INDEX KEY:			0001521163

	FILING VALUES:
		FORM TYPE:		3
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		11891744

	BUSINESS ADDRESS:	
		STREET 1:		AVENIDA JUSCELINO KUBITSCHEK
		STREET 2:		1327 6 ANDAR (PARTE)
		CITY:			SAO PAULO
		STATE:			D5
		ZIP:			04543-000
		BUSINESS PHONE:		55 11 23446284

	MAIL ADDRESS:	
		STREET 1:		AVENIDA JUSCELINO KUBITSCHEK
		STREET 2:		1327 6 ANDAR (PARTE)
		CITY:			SAO PAULO
		STATE:			D5
		ZIP:			04543-000
</SEC-HEADER>
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<TYPE>3
<SEQUENCE>1
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<DESCRIPTION>FORM 3
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<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0203</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2011-06-01</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001521163</rptOwnerCik>
            <rptOwnerName>Raizen Energia Participacoes S.A.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>AVENIDA PRESIDENTE JUSCELINO KUBITSCHECK</rptOwnerStreet1>
            <rptOwnerStreet2>1327 6 O ANDAR</rptOwnerStreet2>
            <rptOwnerCity>SAO PAULO</rptOwnerCity>
            <rptOwnerState>D5</rptOwnerState>
            <rptOwnerZipCode>04543-011</rptOwnerZipCode>
            <rptOwnerStateDescription>BRAZIL</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001517347</rptOwnerCik>
            <rptOwnerName>Ispagnac Participacoes Ltda.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>AVENIDA DAS AMERICAS 4200 BLOCO 6,</rptOwnerStreet1>
            <rptOwnerStreet2>1 O 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>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001306965</rptOwnerCik>
            <rptOwnerName>Royal Dutch Shell plc</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>30, CAREL VAN BYLANDTLAAN</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>THE HAGUE</rptOwnerCity>
            <rptOwnerState>P7</rptOwnerState>
            <rptOwnerZipCode>2596 HR</rptOwnerZipCode>
            <rptOwnerStateDescription>NETHERLANDS</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001430162</rptOwnerCik>
            <rptOwnerName>Cosan S.A. Industria e Comercio</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>AVENIDA PRESIDENTE JUSCELINO KUBITSCHEK,</rptOwnerStreet1>
            <rptOwnerStreet2>1327, 4 O ANDAR</rptOwnerStreet2>
            <rptOwnerCity>SAO PAULO, SP CEP</rptOwnerCity>
            <rptOwnerState>D5</rptOwnerState>
            <rptOwnerZipCode>04543-011</rptOwnerZipCode>
            <rptOwnerStateDescription>BRAZIL</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001402902</rptOwnerCik>
            <rptOwnerName>Cosan Ltd.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>AVENIDA PRESIDENTE JUSCELINO KUBITSCHEK,</rptOwnerStreet1>
            <rptOwnerStreet2>1726 6TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>SAO PAULO, SP</rptOwnerCity>
            <rptOwnerState>D5</rptOwnerState>
            <rptOwnerZipCode>04543-000</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">(1) Acquisition of Codexis Common Stock by Raizen Energia Participacoes S.A. (&quot;Raizen&quot;),  a joint venture company in which Royal Dutch Shell plc (&quot;RDS&quot;) and Cosan Limited are indirectly, through their respective subsidiaries Ispagnac Participacoes Ltda. (&quot;Ispagnac&quot;) and Cosan S.A. Industria e Comercio, joint venture partners, from Ispagnac was part of RDS's and its affiliates' contribution to such joint venture, and was made in exchange for Raizen capital stock.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/  Pedro Isamu Mizutani for Raizen Energia Participacoes S.A as its COO</signatureName>
        <signatureDate>2011-06-01</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/  Matias Lopes for Ispagnac Participacoes Ltda as an Officer</signatureName>
        <signatureDate>2011-06-01</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Mark Edwards for Royal Dutch Shell plc as its Deputy Company Secretary</signatureName>
        <signatureDate>2011-06-01</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/  Marcos Marinho Lutz for Cosan S.A. Industria e Comercio as its CEO</signatureName>
        <signatureDate>2011-06-01</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Rubens Ometo Silveira Mello for Cosan Limited as its CEO</signatureName>
        <signatureDate>2011-06-01</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
