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

    <schemaVersion>X0202</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2007-05-31</periodOfReport>

    <dateOfOriginalSubmission>2007-06-04</dateOfOriginalSubmission>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0000886163</issuerCik>
        <issuerName>LIGAND PHARMACEUTICALS INC</issuerName>
        <issuerTradingSymbol>LGND</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001206367</rptOwnerCik>
            <rptOwnerName>GREETHAM ELIZABETH M</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>10275 SCIENCE CENTER DRIVE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SAN DIEGO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>92121</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2007-05-31</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>5000</value>
                    <footnoteId id="F1"/>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>5000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">On June 4, 2007, a Form 4 was filed on behalf of the reporting person that incorrectly reported the type and amount of securities owned by such person in Table II.  This amended Form 4 is being filed to report the 5,000 shares of common stock acquired by the reporting person on Table I instead of the non-qualified stock option to purchase 10,000 shares of common stock, as reported on the original Form 4.  No stock options were granted to the reporting person on May 31, 2007.

The listed number of shares of common stock were acquired under the issuer's director compensation policy.  This restricted stock award will vest on the first anniversary of the date of grant.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>By: Barbara J. Olson  For: Elizabeth Greetham</signatureName>
        <signatureDate>2007-06-08</signatureDate>
    </ownerSignature>
</ownershipDocument>
