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

    <schemaVersion>X0206</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2015-03-17</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001557421</issuerCik>
        <issuerName>Ignyta, Inc.</issuerName>
        <issuerTradingSymbol>RXDX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000873364</rptOwnerCik>
            <rptOwnerName>CEPHALON INC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>1090 HORSHAM ROAD</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>NORTH WALES</rptOwnerCity>
            <rptOwnerState>PA</rptOwnerState>
            <rptOwnerZipCode>19454</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000818686</rptOwnerCik>
            <rptOwnerName>TEVA PHARMACEUTICAL INDUSTRIES LTD</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>5 BASEL STREET</rptOwnerStreet1>
            <rptOwnerStreet2>PO BOX 3190</rptOwnerStreet2>
            <rptOwnerCity>PETACH TIKVA</rptOwnerCity>
            <rptOwnerState>L3</rptOwnerState>
            <rptOwnerZipCode>4951033</rptOwnerZipCode>
            <rptOwnerStateDescription>ISRAEL</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>3000000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                    <footnoteId id="F1"/>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">Cephalon, Inc. is an indirect wholly owned subsidiary of Teva Pharmaceutical Industries Limited</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Austin D. Kim (Attorney in Fact, Cephalon, Inc.)</signatureName>
        <signatureDate>2015-03-26</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Austin D. Kim (Attorney in Fact, Teva Pharmaceutical Industries Limited)</signatureName>
        <signatureDate>2015-03-26</signatureDate>
    </ownerSignature>
</ownershipDocument>
