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Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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<SEC-DOCUMENT>0000886163-06-000081.txt : 20060921
<SEC-HEADER>0000886163-06-000081.hdr.sgml : 20060921
<ACCEPTANCE-DATETIME>20060921191954
ACCESSION NUMBER:		0000886163-06-000081
CONFORMED SUBMISSION TYPE:	4/A
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20060803
FILED AS OF DATE:		20060921
DATE AS OF CHANGE:		20060921

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			LIGAND PHARMACEUTICALS INC
		CENTRAL INDEX KEY:			0000886163
		STANDARD INDUSTRIAL CLASSIFICATION:	PHARMACEUTICAL PREPARATIONS [2834]
		IRS NUMBER:				770160744
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		10275 SCIENCE CENTER DRIVE
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121-1117
		BUSINESS PHONE:		8585507500

	MAIL ADDRESS:	
		STREET 1:		10275 SCIENCE CENTER DRIVE
		CITY:			SAN DIEGO
		STATE:			CA
		ZIP:			92121-1117

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			BLISSENBACH HENRY F
		CENTRAL INDEX KEY:			0001193124

	FILING VALUES:
		FORM TYPE:		4/A
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-20720
		FILM NUMBER:		061103046

	BUSINESS ADDRESS:	
		STREET 1:		607 POND VIEW DRIVE
		CITY:			MENDOTA HEIGHTS
		STATE:			MN
		ZIP:			55120
		BUSINESS PHONE:		6514546426

	MAIL ADDRESS:	
		STREET 1:		607 POND VIEW DR
		CITY:			MENDOTA HEIGHTS
		STATE:			MN
		ZIP:			55120
</SEC-HEADER>
<DOCUMENT>
<TYPE>4/A
<SEQUENCE>1
<FILENAME>edgardoc.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2006-08-03</periodOfReport>

    <dateOfOriginalSubmission>2006-08-04</dateOfOriginalSubmission>

    <notSubjectToSection16>0</notSubjectToSection16>

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

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001193124</rptOwnerCik>
            <rptOwnerName>BLISSENBACH HENRY F</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>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>President, CEO &amp; Chairman</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Incentive Stock Option (right to buy)</value>
                <footnoteId id="F1"/>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>9.2</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-08-03</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>150000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <footnoteId id="F3"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <footnoteId id="F2"/>
            </exerciseDate>
            <expirationDate>
                <value>2016-08-03</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>150000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>150000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">The 150,000 options granted on August 3, 2006 are Employee Stock Options not Non-Qualified Stock Options as reported on the Form 4 filed on August 4, 2006.</footnote>
        <footnote id="F2">Grant to reporting person of options 50% at 6 months and remaining 50% at the end of one year, except that all of these stock options will vest upon the appointment of the new CEO.</footnote>
        <footnote id="F3">No price applies.</footnote>
    </footnotes>

    <remarks>On August 4, 2006, the reporting person filed a Form 4 which mistakenly included a 7/27/06 grant of 10,000 options which did not in fact occur.</remarks>

    <ownerSignature>
        <signatureName>By: Barbara J. Olson  For: Henry F. Blissenbach</signatureName>
        <signatureDate>2006-09-21</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
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