<?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>0001576113</rptOwnerCik>
            <rptOwnerName>Morenstein Scott D</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CAXTON ALTERNATIVE MANAGEMENT LP</rptOwnerStreet1>
            <rptOwnerStreet2>1330 6TH AVENUE, 20TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10019</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001576081</rptOwnerCik>
            <rptOwnerName>CDK ASSOCIATES, L.L.C.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CAXTON CORPORATION, 731 ALEXANDER</rptOwnerStreet1>
            <rptOwnerStreet2>ROAD, BUILDING #2,  SUITE 500</rptOwnerStreet2>
            <rptOwnerCity>PRINCETON</rptOwnerCity>
            <rptOwnerState>NJ</rptOwnerState>
            <rptOwnerZipCode>08540</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001388551</rptOwnerCik>
            <rptOwnerName>CAXTON CORP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>731 ALEXANDER ROAD, BUILDING #2</rptOwnerStreet1>
            <rptOwnerStreet2>SUITE 500</rptOwnerStreet2>
            <rptOwnerCity>PRINCETON</rptOwnerCity>
            <rptOwnerState>NJ</rptOwnerState>
            <rptOwnerZipCode>08540</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001325713</rptOwnerCik>
            <rptOwnerName>Kovner Bruce</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CAXTON CORPORATION, 731 ALEXANDER</rptOwnerStreet1>
            <rptOwnerStreet2>ROAD, BUILDING #2. SUITE 500</rptOwnerStreet2>
            <rptOwnerCity>PRINCETON</rptOwnerCity>
            <rptOwnerState>NJ</rptOwnerState>
            <rptOwnerZipCode>08540</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1013787</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</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>506893</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>See Footnote</value>
                    <footnoteId id="F1"/>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">These shares are held by CDK Associates, L.L.C. and may be deemed to be beneficially owned by (i) Scott Morenstein, a Managing Director of Caxton Alternative Management LP, the investment manager of CDK Associates, L.L.C., (ii) Caxton Corporation, the manager of CDK Associates, LLC and (iii) Bruce Kovner, the chairman and sole shareholder of Caxton Corporation.  Scott Morenstein serves as a director of the Issuer.  Caxton Corporation, Bruce Kovner and CDK Associates, L.L.C. may be considered directors by deputization due to their affiliation with Scott Morenstein.  Each Reporting Person disclaims beneficial ownership of these shares except to the extent of its or his pecuniary interest, if any, therein, and this report shall not be deemed to be an admission that such Reporting Person is the beneficial owner of such securities for purposes of Section 16 or for any other purpose.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Scott Morenstein</signatureName>
        <signatureDate>2017-08-10</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>CDK Associates, L.L.C., By: Caxton Corporation, its Manager, By: /s/ Heath Weisberg, General Counsel</signatureName>
        <signatureDate>2017-08-10</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Caxton Corporation, By: /s/ Heath Weisberg, General Counsel</signatureName>
        <signatureDate>2017-08-10</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>Bruce Kovner, By: /s/ Heath Weisberg, Attorney-in-Fact</signatureName>
        <signatureDate>2017-08-10</signatureDate>
    </ownerSignature>
</ownershipDocument>
