SECOND AMENDMENT TO ALON USA OPERATING, INC. INCENTIVE STOCK OPTION AGREEMENT

Exhibit 10.16

SECOND AMENDMENT TO
ALON USA OPERATING, INC.
INCENTIVE STOCK OPTION AGREEMENT

     This Amendment is entered into as of November 4, 2008, by and between Alon USA Operating, Inc., a Delaware corporation (the “Corporation”), and Jeff D. Morris (the “Participant”). Terms not defined in this Amendment will have the meaning set forth in the Incentive Stock Option Agreement described below.

     WHEREAS, the Corporation and the Participant entered into an Incentive Stock Option Agreement dated as of July 31, 2000 (the “Agreement”), pursuant to which the Corporation granted to the Participant an option intended to qualify as an incentive stock option within the meaning of Section 422 of the Code to purchase 3,033.4 shares of Common Stock; and

     WHEREAS, the Corporation and the Participant wish to amend the Agreement to assure that the Option does not constitute a deferral of