<SEC-DOCUMENT>0001140361-15-024132.txt : 20150612
<SEC-HEADER>0001140361-15-024132.hdr.sgml : 20150612
<ACCEPTANCE-DATETIME>20150612163747
ACCESSION NUMBER:		0001140361-15-024132
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20141110
FILED AS OF DATE:		20150612
DATE AS OF CHANGE:		20150612

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			CODEXIS INC
		CENTRAL INDEX KEY:			0001200375
		STANDARD INDUSTRIAL CLASSIFICATION:	INDUSTRIAL ORGANIC CHEMICALS [2860]
		IRS NUMBER:				710872999
		FISCAL YEAR END:			1231

	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:			BARUCH THOMAS R
		CENTRAL INDEX KEY:			0001005563

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		15928901

	MAIL ADDRESS:	
		STREET 1:		1 LETTERMAN DRIVE
		STREET 2:		BUILDING C, SUITE CM500
		CITY:			SAN FRANCISCO
		STATE:			CA
		ZIP:			94129
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>doc1.xml
<DESCRIPTION>FORM 4
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2014-11-10</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001005563</rptOwnerCik>
            <rptOwnerName>BARUCH THOMAS R</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CODEXIS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>200 PENOBSCOT DRIVE</rptOwnerStreet2>
            <rptOwnerCity>REDWOOD CITY</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94063</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle></officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>138451</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2014-11-10</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>2740158</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F2"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2014-11-10</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F3"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>181067</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F4"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable></derivativeTable>

    <footnotes>
        <footnote id="F1">The shares were sold by CMEA Ventures Life Sciences 2000, L.P. (&quot;CMEA LS&quot;) to Presidio Partners 2014, L.P. for $2.37 per share.  The reported transaction is the same transaction reported by CMEA LS in its capacity as a 10% holder of the Issuer's securities in a separate Form 4 filed on Nov 12, 2014.</footnote>
        <footnote id="F2">The shares are held by CMEA LS.  Thomas R. Baruch, a member of the Issuer's board of directors, is a general partner of CMEA Ventures LS Management 2000, L.P., the general partner of CMEA LS, and, as such, has voting and investment power over the securities held by CMEA LS. The Reporting Person disclaims beneficial ownership of the securities reported on this Form 4 except to the extent of any pecuniary interest therein.</footnote>
        <footnote id="F3">The shares were sold by CMEA Ventures Life Sciences 2000, Civil Law Partnership (&quot;CMEA CLP&quot;) to Presidio Partners 2014, L.P. for $2.37 per share.  The reported transaction is the same transaction reported by CMEA CLP in its capacity as a 10% holder of the Issuer's securities in a separate Form 4 filed on Nov 12, 2014.</footnote>
        <footnote id="F4">The shares are held by CMEA CLP. Thomas R. Baruch, a member of the Isser's board of directors, is a general partner of CMEA Ventures LS Management 2000, L.P., the managing limited partner of CMEA CLP, and, as such, has voting and investment power over the securities held by CMEA CLP. The Reporting Person disclaims beneficial ownership of the securities reported on this Form 4 except to the extent of any pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Doug Sheehy, Attorney-in-Fact for Thomas Baruch</signatureName>
        <signatureDate>2015-06-12</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
