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

    <schemaVersion>X0306</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2019-08-06</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>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>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Warrant</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.00</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2019-08-06</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>D</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>30666667</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2018-02-05</value>
            </exerciseDate>
            <expirationDate>
                <value>2020-12-31</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>30666667</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Warrant</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.00</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2019-08-06</value>
            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
            </transactionCoding>
            <transactionTimeliness>
                <value></value>
            </transactionTimeliness>
            <transactionAmounts>
                <transactionShares>
                    <value>30666667</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F2"/>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
                <footnoteId id="F3"/>
            </exerciseDate>
            <expirationDate>
                <value>2021-12-31</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>30666667</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>30666667</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">These securities of Marrone Bio Innovations, Inc. (the &quot;Issuer&quot;) are or were held by Ospraie Ag Science LLC (&quot;Ospraie LLC&quot;). Mr. Dwight Anderson (&quot;Mr. Anderson&quot;) is the Managing Member of Ospraie LLC and, in such capacity, may be deemed to have voting and dispositive power over the securities held for the account 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>
        <footnote id="F2">On August 6, 2019, the Issuer, Ospraie LLC, Ardsley Partners Renewable Energy Fund, L.P. and Ivan Saval entered into a Warrant Amendment and Plan of Reorganization Agreement (the &quot;Agreement&quot;) pursuant to which the expiration date of the warrants to purchase common stock of the Issuer held by Ospraie LLC was extended to December 31, 2021.  In addition, pursuant to the Agreement, the Issuer will have a right, so long as the closing price for the Issuer's common stock on its principal market immediately prior to the exercise of such right is in excess of the exercise price for the warrants, to require Ospraie LLC to exercise up to all of its warrants in exchange for the shares of common stock underlying such warrants and new warrants (&quot;New Warrants&quot;) to purchase shares of common stock of the Issuer in an amount equal to the amount of warrants being required to be exercised.</footnote>
        <footnote id="F3">(Continued from footnote 2) Such New Warrants will be first exercisable 180 days after issuance, will have a term expiring on January 1, 2023 and will have an exercise price of $1.75 per share.  The transactions reported herein were approved in advance by the Issuer's Board of Directors.</footnote>
    </footnotes>

    <remarks>Each of Ospraie Ag Science LLC and Mr. Anderson 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>2019-08-08</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Dwight Anderson</signatureName>
        <signatureDate>2019-08-08</signatureDate>
    </ownerSignature>
</ownershipDocument>
