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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2017-08-01</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001183765</issuerCik>
        <issuerName>Molecular Templates, Inc.</issuerName>
        <issuerTradingSymbol>MTEM</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001622968</rptOwnerCik>
            <rptOwnerName>SHV Management Services, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SANTE VENTURES</rptOwnerStreet1>
            <rptOwnerStreet2>300 W 6TH STREET, SUITE 2300</rptOwnerStreet2>
            <rptOwnerCity>AUSTIN</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>78701</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001623014</rptOwnerCik>
            <rptOwnerName>Cunningham Joe H</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SANTE VENTURES</rptOwnerStreet1>
            <rptOwnerStreet2>300 W 6TH STREET, SUITE 2300</rptOwnerStreet2>
            <rptOwnerCity>AUSTIN</rptOwnerCity>
            <rptOwnerState></rptOwnerState>
            <rptOwnerZipCode>78701</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001198064</rptOwnerCik>
            <rptOwnerName>FRENCH DOUGLAS D</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O SANTE VENTURES</rptOwnerStreet1>
            <rptOwnerStreet2>300 W 6TH STREET, SUITE 2300</rptOwnerStreet2>
            <rptOwnerCity>AUSTIN</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>78701</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001622969</rptOwnerCik>
            <rptOwnerName>SHV Management Services, LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>300 W 6TH STREET, SUITE 2300</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>AUSTIN</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>78701</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001433076</rptOwnerCik>
            <rptOwnerName>SANTE HEALTH VENTURES I LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>300 W 6TH STREET, SUITE 2300</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>AUSTIN</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>78701</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001640842</rptOwnerCik>
            <rptOwnerName>Sante Health Ventures I Annex Fund, LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>300 W 6TH STREET, SUITE 2300</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>AUSTIN</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>78701</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>7897298</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>Held by Sante Health Ventures I, L.P.</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>864665</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>Held by Sante Health Ventures I Annex Fund, L.P.</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>Warrants</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.8423</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2017-08-01</value>
            </exerciseDate>
            <expirationDate>
                <value>2024-08-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>19310</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>Held by Sante Health Ventures I, L.P.</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>Warrants</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.8423</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2017-08-01</value>
            </exerciseDate>
            <expirationDate>
                <value>2024-08-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>4827</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>Held by Sante Health Ventures I Annex Fund, L.P.</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The securities held by Sante Health Ventures I, L.P. and Sante Health Ventures I Annex Fund, L.P. may be deemed to be beneficially owned by Joe Cunningham, M.D. and Douglas D. French, who are managing directors (the &quot;SHV Directors&quot;) of SHV Management Services, LLC (&quot;SHV Management&quot;). SHV Management is the general partner of SHV Management Services, LP, which is the general partner of Sante Health Ventures I, L.P., and SHV Annex Services, LP, which is the general partner of Sante Health Ventures I Annex Fund, L.P. Each of the SHV Directors, SHV Management, SHV Management Services, LP and SHV Annex Services, LP disclaims beneficial ownership of the reported securities except to the extent of his or its pecuniary interest therein.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>SHV MANAGEMENT SERVICES, LLC, By: Kevin Lalande, Its Managing Member, By: /s/ Jason S. Kim, Attorney in fact</signatureName>
        <signatureDate>2017-08-11</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>SHV MANAGEMENT SERVICES, L.P., By: SHV Management Services, LLC, Its general partner, By: Kevin Lalande, Its Managing Member, By: /s/ Jason S. Kim, Attorney in fact</signatureName>
        <signatureDate>2017-08-11</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>SANTE HEALTH VENTURES I, L.P., By:  SHV Management Services, L.P., Its general partner, By: SHV Management Services, LLC, Its general partner, By: Kevin Lalande, Its Managing Member, By: /s/ Jason S. Kim, Attorney in fact</signatureName>
        <signatureDate>2017-08-11</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>SANTE HEALTH VENTURES I ANNEX FUND, L.P., By:	SHV Annex Services, LP, Its general partner, By: SHV Management Services, LLC, Its general partner, By:	Kevin Lalande, Its Managing Member, By:	/s/ Jason S. Kim, Attorney in fact</signatureName>
        <signatureDate>2017-08-11</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>JOE CUNNINGHAM, MD, By:	/s/ Jason S. Kim, Attorney-in-Fact</signatureName>
        <signatureDate>2017-08-11</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>DOUGLAS D. FRENCH, By: /s/ Jason S. Kim, Attorney in fact</signatureName>
        <signatureDate>2017-08-11</signatureDate>
    </ownerSignature>
</ownershipDocument>
