<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2017-01-04</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001478121</issuerCik>
        <issuerName>Pfenex Inc.</issuerName>
        <issuerTradingSymbol>PFNX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001433536</rptOwnerCik>
            <rptOwnerName>SIGNET HEALTHCARE PARTNERS ACCREDITED PARTNERSHIP III LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>152 WEST 57TH STREET</rptOwnerStreet1>
            <rptOwnerStreet2>19TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10019</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, par value $0.001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2017-01-04</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>4765</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>9.5012</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1708302</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2017-01-05</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1049</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>9.5113</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1707253</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2017-01-04</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1554</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>9.5012</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>557096</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, par value $0.001 per share</value>
            </securityTitle>
            <transactionDate>
                <value>2017-01-05</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>S</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>342</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>9.5113</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>556754</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F2"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Beneficially owned directly by Signet Healthcare Partners QP Partnership III LP (&quot;SHPQP3&quot;) and indirectly by Signet Healthcare GP III LP, the general partner of SHPQP3; Signet Healthcare Partners LP, the management company for SHPQP3; and Signet Holdings LLC, the general partner of Signet Healthcare GP III LP and Signet Healthcare Partners LP. Signet Healthcare Partners LP, Signet Healthcare GP III LP and Signet Holdings LLC disclaim beneficial ownership of the reported securities except to the extent of their pecuniary interest therein, if any.</footnote>
        <footnote id="F2">Beneficially owned directly by Signet Healthcare Partners Accredited Partnership III LP (&quot;SHPAP3&quot;) and indirectly by Signet Healthcare GP III LP, the general partner of SHPAP3; Signet Healthcare Partners LP, the management company for SHPAP3; and Signet Holdings LLC, the general partner of Signet Healthcare GP III LP and Signet Healthcare Partners LP. Signet Healthcare Partners LP, Signet Healthcare GP III LP and Signet Holdings LLC disclaim beneficial ownership of the reported securities except to the extent of their pecuniary interest therein, if any.</footnote>
    </footnotes>

    <remarks>This is a joint filing by Signet Healthcare Partners Accredited Partnership III LP, Signet Healthcare Partners QP Partnership III LP, Signet Healthcare GP III LP, Signet Healthcare Partners LP and Signet Holdings LLC. Signet Healthcare Partners Accredited Partnership III LP is the designated filer for Signet Healthcare Partners QP Partnership III LP. Signet Healthcare GP III LP, Signet Healthcare Partners LP, and Signet Holdings LLC. The address of each filer is the same as the designated filer. See notes 1 and 2 above. Signet Healthcare Partners LP, Signet Healthcare GP III LP, and Signet Holdings LLC disclaim beneficial ownership of such shares except to the extent of their pecuniary interest therein, if any.</remarks>

    <ownerSignature>
        <signatureName>/s/ James C. Gale, Chief Investment Officer of Signet Holdings, LLC, the general partner of Signet Healthcare GP III, LP, the general partner of Signet Healthcare Partners Accredited
   Partnership III LP</signatureName>
        <signatureDate>2017-01-06</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ James C. Gale, Chief Investment Officer of Signet Holdings, LLC, the general partner of Signet Healthcare GP III, LP, the general partner of the Signet Healthcare Partners QP
   Partnership III LP</signatureName>
        <signatureDate>2017-01-06</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ James C. Gale, Chief Investment Officer of Signet Holdings, LLC, the general partner of Signet Healthcare Partners LP and Signet Healthcare GP III LP</signatureName>
        <signatureDate>2017-01-06</signatureDate>
    </ownerSignature>
</ownershipDocument>
