Zeolites NaY, HUSY and KL were ion-exchanged with a cationic molybdenum sulfide cluster [Mo3S4(H2O)(9)](4+) with incomplete cubane-type structure and a cationic nickel-molybdenum mixed sulfide cluster [Mo3NiS4Cl(H2O)(9)](3+) with complete cubane-type structure. The UV-visible spectra and EXAFS analysis data exhibited that the structure of the molybdenum cluster was maintained after ion exchange. These zeolite catalysts showed activity for benzothiophene hydrodesulfurization; especially, involvement of Ni resulted in great enhancement of the hydrodesulfurization activity.