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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2020-09-15</periodOfReport>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001441693</issuerCik>
        <issuerName>MARRONE BIO INNOVATIONS INC</issuerName>
        <issuerTradingSymbol>MBII</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001730557</rptOwnerCik>
            <rptOwnerName>Ospraie Ag Science LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O DWIGHT ANDERSON</rptOwnerStreet1>
            <rptOwnerStreet2>437 MADISON AVENUE, 28TH FLOOR</rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10022</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>See Remarks</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001326533</rptOwnerCik>
            <rptOwnerName>Ospraie Management, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>437 MADISON AVENUE, 28TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10022</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>See Remarks</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001392205</rptOwnerCik>
            <rptOwnerName>Ospraie Holding I, L.P.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>437 MADISON AVENUE, 28TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10022</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>See Remarks</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001392203</rptOwnerCik>
            <rptOwnerName>Ospraie Management, Inc.</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>437 MADISON AVENUE, 28TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10022</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>See Remarks</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001392202</rptOwnerCik>
            <rptOwnerName>Anderson Dwight</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>437 MADISON AVENUE, 28TH FLOOR</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>NEW YORK</rptOwnerCity>
            <rptOwnerState>NY</rptOwnerState>
            <rptOwnerZipCode>10022</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>See Remarks</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock, $0.00001 par value</value>
            </securityTitle>
            <transactionDate>
                <value>2020-09-15</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1974213</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.75</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>53542155</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Warrant</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>0.75</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2020-09-15</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>1974213</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F1"/>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2020-04-29</value>
            </exerciseDate>
            <expirationDate>
                <value>2020-09-15</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>1974213</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">On September 15, 2020, Ospraie Ag Science LLC (&quot;Ospraie LLC&quot;) exercised warrants to purchase Common Stock of Marrone Bio Innovations, Inc. (the &quot;Issuer&quot;) and purchased the 1,974,213 shares of Issuer Common Stock underlying such warrants.</footnote>
        <footnote id="F2">Ospraie Management, LLC (&quot;Ospraie Management&quot;) is the investment manager of Ospraie LLC and has been delegated voting and investment power and thus beneficial ownership of the shares of Common Stock of the Issuer and warrants to purchase shares of Common Stock of the Issuer held by Ospraie LLC.  Ospraie Holding I, LP (&quot;Ospraie Holding&quot;) may be deemed to beneficially own the shares of Common Stock of the Issuer and warrants to purchase shares of Common Stock of the Issuer held by Ospraie LLC as the managing member of Ospraie Management. Ospraie Management, Inc. (&quot;Ospraie Inc.&quot;) may be deemed to beneficially own the shares of Common Stock of the Issuer and warrants to purchase Common Stock of the Issuer held by Ospraie LLC as the general partner of Ospraie Holding.</footnote>
        <footnote id="F3">(Continued from footnote 2) Dwight Anderson may be deemed to beneficially own the shares of Common Stock of the Issuer and warrants to purchase Common Stock of the Issuer held by Ospraie LLC as the Managing Principal of Ospraie Management, the sole owner of Ospraie Inc. and the sole managing member of Ospraie LLC.  Each Reporting Person disclaims beneficial ownership of the securities reported herein except to the extent of his or its pecuniary interest therein, if any.</footnote>
    </footnotes>

    <remarks>Each of Ospraie Ag Science LLC, Ospraie Management, LLC, Ospraie Holding I, LP, Ospraie Management, Inc. and Dwight Anderson (collectively, the &quot;Reporting Persons&quot;) may be deemed a director by deputization of Marrone Bio Innovations, Inc. (the &quot;Issuer&quot;) by virtue of the fact that Messrs. Robert A. Woods, Yogesh Mago, Keith McGovern and Stuart Woolf, representatives of the Reporting Persons, currently serve on the board of directors of the Issuer.</remarks>

    <ownerSignature>
        <signatureName>OSPRAIE AG SCIENCE LLC, Name: /s/ Dwight Anderson, Title: Managing Member</signatureName>
        <signatureDate>2020-10-13</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>OSPRAIE MANAGEMENT, LLC, By: Ospraie Holding I, L.P., its managing member, By: Ospraie Management, Inc., its general partner, Name: /s/ Dwight Anderson, Title: Sole Owner</signatureName>
        <signatureDate>2020-10-13</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>OSPRAIE HOLDING I, LP, By: Ospraie Management, Inc., its general partner, Name: /s/ Dwight Anderson, Title: Sole Owner</signatureName>
        <signatureDate>2020-10-13</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>OSPRAIE MANAGEMENT, INC., Name: /s/ Dwight Anderson, Title: Sole Owner</signatureName>
        <signatureDate>2020-10-13</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>DWIGHT ANDERSON, Name: /s/ Dwight Anderson</signatureName>
        <signatureDate>2020-10-13</signatureDate>
    </ownerSignature>
</ownershipDocument>
