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

    <schemaVersion>X0203</schemaVersion>

    <documentType>3</documentType>

    <periodOfReport>2008-10-13</periodOfReport>

    <noSecuritiesOwned>0</noSecuritiesOwned>

    <issuer>
        <issuerCik>0001273013</issuerCik>
        <issuerName>PHARMACOPEIA INC</issuerName>
        <issuerTradingSymbol>PCOP</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001319763</rptOwnerCik>
            <rptOwnerName>El Coronado Holdings, LLC</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>4673 CHRISTOPHER PLACE</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>DALLAS</rptOwnerCity>
            <rptOwnerState>TX</rptOwnerState>
            <rptOwnerZipCode>75204</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>1</isTenPercentOwner>
            <isOther>0</isOther>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeHolding>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>4070164</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeHolding>
    </nonDerivativeTable>

    <footnotes></footnotes>

    <remarks>This report is filed on behalf of El Coronado Holdings, LLC (&quot;ECH&quot;), an Arizona limited liability company of which Josiah T. Austin is the sole managing member.  The address of ECH is 4673 Christopher Place, Dallas, Texas, 75204.  ECH owns directly all 4,070,164 shares of common stock identified in Table I.  Mr. Austin has previously filed a Form 4 covering  the shares of common stock held by ECH identified in Table I.</remarks>

    <ownerSignature>
        <signatureName>Josiah T. Austin, as Sole Managing Member of ECH</signatureName>
        <signatureDate>2008-10-23</signatureDate>
    </ownerSignature>
</ownershipDocument>
