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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2021-03-29</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <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>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2021-03-29</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>80000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>11.4481</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>8116105</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </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.  This Form 4 is filed jointly by BB Biotech AG and Biotech Target N.V.</remarks>

    <ownerSignature>
        <signatureName>/s/ Ivo Betschart</signatureName>
        <signatureDate>2021-03-31</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Martin Gubler</signatureName>
        <signatureDate>2021-03-31</signatureDate>
    </ownerSignature>
</ownershipDocument>
