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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2020-10-26</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001259870</rptOwnerCik>
            <rptOwnerName>BIOTECH TARGET N V</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>ARA HILL TOP BUILDING, UNIT A-5,</rptOwnerStreet1>
            <rptOwnerStreet2>PLETTERIJWEG OOST 1</rptOwnerStreet2>
            <rptOwnerCity>CURACAO</rptOwnerCity>
            <rptOwnerState>P8</rptOwnerState>
            <rptOwnerZipCode>00000</rptOwnerZipCode>
            <rptOwnerStateDescription>NETHERLANDS ANTILLES</rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000924223</rptOwnerCik>
            <rptOwnerName>BB BIOTECH AG</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>SCHWERTSTRASSE 6</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SCHAFFHAUSEN</rptOwnerCity>
            <rptOwnerState>V8</rptOwnerState>
            <rptOwnerZipCode>CH-8200</rptOwnerZipCode>
            <rptOwnerStateDescription>SWITZERLAND</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>5069996</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes></footnotes>

    <remarks>Biotech Target N.V. is a wholly-owned subsidiary of BB Biotech AG. Accordingly, BB Biotech AG may be deemed to be the indirect beneficial owner of the securities of Molecular Templates, Inc. held directly or indirectly by Biotech Target N.V. The Form 3 is jointly filed by BB Biotech AG and Biotech Target N.V.</remarks>

    <ownerSignature>
        <signatureName>/s/ Martin Gubler</signatureName>
        <signatureDate>2020-11-02</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Ivo Betschart</signatureName>
        <signatureDate>2020-11-02</signatureDate>
    </ownerSignature>
</ownershipDocument>
