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

    <schemaVersion>X0204</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2011-08-30</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001093207</issuerCik>
        <issuerName>CROSSROADS SYSTEMS INC</issuerName>
        <issuerTradingSymbol>CRDS</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001310607</rptOwnerCik>
            <rptOwnerName>Bianchi Brian Joseph</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>C/O CROSSROADS SYSTEMS, INC.</rptOwnerStreet1>
            <rptOwnerStreet2>11000 NORTH MO-PAC EXPRESSWAY</rptOwnerStreet2>
            <rptOwnerCity>AUSTIN</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>78759</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>Chief Operating Officer</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>COMMON STOCK</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>101950</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeHolding>
            <securityTitle>
                <value>OPTION (RIGHT TO BUY)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>3.52</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-03-31</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>COMMON STOCK</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>12044</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>OPTION (RIGHT TO BUY)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>4.48</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2017-01-31</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>COMMON STOCK</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>43991</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>OPTION (RIGHT TO BUY)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>4.56</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2015-08-31</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>COMMON STOCK</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>12250</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>OPTION (RIGHT TO BUY)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>5.56</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-09-29</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>COMMON STOCK</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>11001</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>OPTION (RIGHT TO BUY)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>6.20</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2012-05-31</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>COMMON STOCK</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>13751</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>OPTION (RIGHT TO BUY)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>7.48</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2013-08-21</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>COMMON STOCK</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>5175</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>OPTION (RIGHT TO BUY)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>10.64</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-02-04</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>COMMON STOCK</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>12500</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>OPTION (RIGHT TO BUY)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.56</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2020-08-25</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>COMMON STOCK</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>12500</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
        <derivativeHolding>
            <securityTitle>
                <value>OPTION (RIGHT TO BUY)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>1.56</value>
            </conversionOrExercisePrice>
            <exerciseDate>
                <value>2012-08-25</value>
            </exerciseDate>
            <expirationDate>
                <value>2020-08-25</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>COMMON STOCK</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>12500</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeHolding>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">These options are fully vested.</footnote>
        <footnote id="F2">These options vest over four years with 25% vesting August 2011 and the remainder vesting over three years thereafter in quarterly installments.</footnote>
    </footnotes>

    <remarks>Exhibit 24 - Power of Attorney</remarks>

    <ownerSignature>
        <signatureName>/s/Jennifer Crane, Attorney-in-Fact</signatureName>
        <signatureDate>2011-08-30</signatureDate>
    </ownerSignature>
</ownershipDocument>
