<SUBMISSION>
<ACCESSION-NUMBER>0001179044-04-000069
<TYPE>4
<PUBLIC-DOCUMENT-COUNT>1
<PERIOD>20040510
<FILING-DATE>20040514
<REPORTING-OWNER>
<OWNER-DATA>
<CONFORMED-NAME>LEVY RICARDO B
<CIK>0000942916
</OWNER-DATA>
<FILING-VALUES>
<FORM-TYPE>4
<ACT>34
<FILE-NUMBER>000-27188
<FILM-NUMBER>04807010
</FILING-VALUES>
<BUSINESS-ADDRESS>
<STREET1>430 FERGUSON DR
<CITY>MOUNTAIN VIEW
<STATE>CA
<ZIP>94043
</BUSINESS-ADDRESS>
</REPORTING-OWNER>
<ISSUER>
<COMPANY-DATA>
<CONFORMED-NAME>PHARMACOPEIA INC
<CIK>0001002388
<ASSIGNED-SIC>7372
<IRS-NUMBER>330557266
<STATE-OF-INCORPORATION>DE
<FISCAL-YEAR-END>1231
</COMPANY-DATA>
<BUSINESS-ADDRESS>
<STREET1>CN 5350
<CITY>PRINCETON
<STATE>NJ
<ZIP>08543-5350
<PHONE>6094523600
</BUSINESS-ADDRESS>
<MAIL-ADDRESS>
<STREET1>CN 5350
<CITY>PRINCETON
<STATE>NJ
<ZIP>08543-5350
</MAIL-ADDRESS>
</ISSUER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2004-05-10</periodOfReport>

    <issuer>
        <issuerCik>0001002388</issuerCik>
        <issuerName>PHARMACOPEIA INC</issuerName>
        <issuerTradingSymbol>ACCL</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0000942916</rptOwnerCik>
            <rptOwnerName>LEVY RICARDO B</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>9685 SCRANTON ROAD</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>2004-05-12</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>P</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>3000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>10.35</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>3000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Nonstatutory Stock Option (right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>9.35</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2004-05-10</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>A</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>20000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2005-05-10</value>
                <footnoteId id="F1"/>
            </exerciseDate>
            <expirationDate>
                <value>2014-05-09</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>20000</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>20000</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Grant to reporting person of option to purchase shares of Common Stock pursuant to the issuer's 1995 Director Stock Option Plan.  One-third of the shares subject to the option vest annually commencing on 5/10/05 such that all shares will be completely vested on 5/10/07.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>Ricardo B. Levy</signatureName>
        <signatureDate>2004-05-13</signatureDate>
    </ownerSignature>
</ownershipDocument>

</XML>
</TEXT>
</DOCUMENT>
</SUBMISSION>
