<SEC-DOCUMENT>0001209191-14-068117.txt : 20141112
<SEC-HEADER>0001209191-14-068117.hdr.sgml : 20141111
<ACCEPTANCE-DATETIME>20141112163156
ACCESSION NUMBER:		0001209191-14-068117
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20141110
FILED AS OF DATE:		20141112
DATE AS OF CHANGE:		20141112

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:			CMEA VENTURES LIFE SCIENCES 2000 LP
		CENTRAL INDEX KEY:			0001127950

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		141214502

	BUSINESS ADDRESS:	
		STREET 1:		235 MONTGOMERY ST
		STREET 2:		STE 920
		CITY:			SAN FRANCISCO
		STATE:			CA
		ZIP:			94104

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			CMEA Ventures Life Sciences 2000, Civil Law Partnership
		CENTRAL INDEX KEY:			0001425388

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		141214503

	BUSINESS ADDRESS:	
		STREET 1:		ONE EMBARCADERO CENTER
		STREET 2:		SUITE 3250
		CITY:			SAN FRANCISCO
		STATE:			CA
		ZIP:			94111
		BUSINESS PHONE:		415-352-1520

	MAIL ADDRESS:	
		STREET 1:		ONE EMBARCADERO CENTER
		STREET 2:		SUITE 3250
		CITY:			SAN FRANCISCO
		STATE:			CA
		ZIP:			94111

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Handelsman Karl D.
		CENTRAL INDEX KEY:			0001425381

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		141214504

	MAIL ADDRESS:	
		STREET 1:		C/O CMEA VENTURES
		STREET 2:		ONE EMBARCADERO CENTER, SUITE 3250
		CITY:			SAN FRANCISCO
		STATE:			CA
		ZIP:			94111

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Collier David J
		CENTRAL INDEX KEY:			0001340886

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		141214505

	MAIL ADDRESS:	
		STREET 1:		C/O CMEA VENTURES
		STREET 2:		ONE EMBARCADERO CENTER, SUITE 3250
		CITY:			SAN FRANCISCO
		STATE:			CA
		ZIP:			94111

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			CMEA Ventures LS Management 2000, L.P.
		CENTRAL INDEX KEY:			0001425387

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-34705
		FILM NUMBER:		141214506

	BUSINESS ADDRESS:	
		STREET 1:		ONE EMBARCADERO CENTER
		STREET 2:		SUITE 3250
		CITY:			SAN FRANCISCO
		STATE:			CA
		ZIP:			94111
		BUSINESS PHONE:		415-352-1520

	MAIL ADDRESS:	
		STREET 1:		ONE EMBARCADERO CENTER
		STREET 2:		SUITE 3250
		CITY:			SAN FRANCISCO
		STATE:			CA
		ZIP:			94111
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>doc4.xml
<DESCRIPTION>FORM 4 SUBMISSION
<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>0001127950</rptOwnerCik>
            <rptOwnerName>CMEA VENTURES LIFE SCIENCES 2000 LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3250</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001425388</rptOwnerCik>
            <rptOwnerName>CMEA Ventures Life Sciences 2000, Civil Law Partnership</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3250</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001425387</rptOwnerCik>
            <rptOwnerName>CMEA Ventures LS Management 2000, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3250</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001340886</rptOwnerCik>
            <rptOwnerName>Collier David J</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3250</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001425381</rptOwnerCik>
            <rptOwnerName>Handelsman Karl D.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ONE EMBARCADERO CENTER</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 3250</rptOwnerStreet2>
            <rptOwnerCity>SAN FRANCISCO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94111</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2014-11-10</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>2740158</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>2.37</value>
                </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="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2014-11-10</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>181067</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>2.37</value>
                </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>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Held by CMEA Ventures Life Sciences 2000, L.P.  Thomas R. Baruch, a member of the Issuer's board of directors, David Collier and Karl Handelsman are general partners of CMEA Ventures LS Management 2000, L.P., the general partner of CMEA Ventures Life Sciences 2000, L.P., and, as such, have voting and investment power over the securities held by CMEA Ventures Life Sciences 2000, L.P.  Each of the Reporting Persons disclaims beneficial ownership of the securities reported on this Form 4 except to the extent of any pecuniary interest therein.</footnote>
        <footnote id="F2">Held by CMEA Ventures Life Sciences 2000, Civil Law Partnership. Thomas R. Baruch, a member of the Isser's board of directors, David Collier and Karl Handelsman are general partners of CMEA Ventures LS Management 2000, L.P., the managing limited partner of CMEA Ventures Life Sciences 2000, Civil Law Partnership, and, as such, have voting and investment power over the securities held by CMEA Ventures Life Sciences 2000, Civil Law Partnership.  Each of the Reporting Persons disclaims beneficial ownership of the securities reports on this Form 4 except to the extent of any pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>CMEA Ventures Life Sciences 2000, LP
By:CMEA Ventures LS Management 2000, LP
for CMEA Ventures Life Sciences 2000, L.P., as its General Partner
/s/ David Collier</signatureName>
        <signatureDate>2014-11-12</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Thomas R. Baruch</signatureName>
        <signatureDate>2014-11-12</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Thomas R. Baruch</signatureName>
        <signatureDate>2014-11-12</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ David Collier</signatureName>
        <signatureDate>2014-11-12</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Karl D. Handelsman</signatureName>
        <signatureDate>2014-11-12</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
