EXHIBIT 32.2



                    CERTIFICATION BY CHIEF FINANCIAL OFFICER
                       PURSUANT TO 18 U.S.C. SECTION 1350,
                       AS ADOPTED PURSUANT TO SECTION 906
                        OF THE SARBANES-OXLEY ACT OF 2002

     In connection with the accompanying Quarterly Report on Form 10-Q of Ligand
Pharmaceuticals Inc. for the quarter ended June 30, 2004, I, Paul V. Maier,
Senior Vice President, Chief Financial Officer of Ligand Pharmaceuticals Inc.,
hereby certify pursuant to 18 U.S.C. Section 1350, as adopted pursuant to
Section 906 of the Sarbanes-Oxley Act of 2002, to the best of my knowledge and
belief, that:

     (1) such Quarterly Report on Form 10-Q for the quarter ended June 30, 2004,
fully complies with the requirements of section 13(a) or 15(d) of the Securities
Exchange Act of 1934; and

     (2) the information contained in such Quarterly Report on Form 10-Q for the
quarter ended June 30, 2004, fairly presents, in all material respects, the
financial condition and results of operations of Ligand Pharmaceuticals Inc.

     The foregoing certification is being furnished solely to accompany the
Report pursuant to 18 U.S.C. ss. 1350, and is not being filed for purposes of
Section 18 of the Securities Exchange Act of 1934, as amended, and is not to be
incorporated by reference into any filing of the Company, whether made before or
after the date hereof, regardless of any general incorporation language in such
filing.

Date: August 5, 2004            /S/ PAUL V. MAIER
                                  ---------------------------------------------
                                  Paul V. Maier
                                  SENIOR VICE PRESIDENT, CHIEF FINANCIAL OFFICER