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    <periodOfReport>2013-09-11</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0001356857</issuerCik>
        <issuerName>Trius Therapeutics Inc</issuerName>
        <issuerTradingSymbol>TSRX</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001478916</rptOwnerCik>
            <rptOwnerName>Schmid John P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O TRIUS THERAPEUTICS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>6310 NANCY RIDGE DR, # 105</rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Financial Officer</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

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    <derivativeTable>
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            <expirationDate>
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            <expirationDate>
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            <transactionTimeliness>
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                <transactionShares>
                    <value>75000</value>
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                <transactionPricePerShare>
                    <value>10.00</value>
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            <expirationDate>
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                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>75000</value>
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        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
            </securityTitle>
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                <value>4.80</value>
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            <transactionDate>
                <value>2013-09-11</value>
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            <deemedExecutionDate></deemedExecutionDate>
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            <transactionTimeliness>
                <value></value>
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            <transactionAmounts>
                <transactionShares>
                    <value>85000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>8.70</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
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            <exerciseDate>
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            <expirationDate>
                <value>2022-03-07</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>85000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
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        <derivativeTransaction>
            <securityTitle>
                <value>Stock Option (right to buy)</value>
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            <conversionOrExercisePrice>
                <value>6.13</value>
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            <transactionDate>
                <value>2013-09-11</value>
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            <deemedExecutionDate></deemedExecutionDate>
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            <transactionTimeliness>
                <value></value>
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            <transactionAmounts>
                <transactionShares>
                    <value>140000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>7.37</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
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            <exerciseDate>
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            <expirationDate>
                <value>2023-03-06</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
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                <underlyingSecurityShares>
                    <value>140000</value>
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                    <value>0</value>
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    <footnotes>
        <footnote id="F1">Pursuant the terms of that certain Agreement and Plan of Merger, dated as of July 30, 2013, by and among Trius Therapeutics, Inc., Cubist Pharmaceuticals, Inc., and BRGO Corporation  (the &quot;Merger Agreement&quot;) and the Offer (as defined in the Merger Agreement), each share of Trius common stock was validly tendered for $13.50 per share in cash plus one non-transferrable contingent value right for each share (each a &quot;CVR&quot;), which represents the contractual right to receive up to $2.00 per share upon the achievement of certain milestones, subject to any required withholding of taxes.</footnote>
        <footnote id="F2">Pursuant the terms of the Merger Agreement and the Offer, each stock option that was outstanding and unexercised as of the Offer Acceptance Time (as defined in the Merger Agreement), whether or not vested, was cancelled and converted into the right to receive $13.50 per share (minus the exercise price of the option) in cash plus one CVR which represents the contractual right to receive up to $2.00 per share upon the achievement of certain milestones, subject to any required withholding of taxes.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Michael Morneau, Attorney-in-Fact</signatureName>
        <signatureDate>2013-09-12</signatureDate>
    </ownerSignature>
</ownershipDocument>
