Molybdenum sulfide cluster [Mo3S4(H2O)(9)](4+) and nickel-molybdenum bimetallic sulfide cluster [Mo3NiS4Cl(H2O)(9)](3+) were incorporated into zeolites NaY, HUSY, NaH beta, Na-mordenite (NaMOR), and KL by aqueous ion exchange. EXAFS data revealed that the structure of the molybdenum sulfide cluster remained virtually intact after ion exchange, However, the incomplete cubane-type structure of the cluster might be lost after thermal treatment at 573 K. The structure of the cluster in Mo3S4/NaY and Mo3S4/KL seems to have changed to the MoS2-like structure through the hydrodesulfurization (HDS) reaction, although a considerably high level of dispersion was kept. Mo3S4 cluster catalysts loaded on NaMOR and KL exhibited a higher level of activity for HDS of benzothiophene than Mo3S4 catalysts loaded on the other zeolites. Benzene was formed through acid-catalyzed dealkylation of ethylbenzene, the primary HDS product. Alkylation of benzothiophene with alkenes derived from the cracking of decane as the solvent also occurred, The acidity seems to be produced through the ion exchange and reduction of cationic clusters during activation. Over HUSY- and NaH beta-supported catalysts benzene was the major HDS product, Nickel incorporation into the Mo3S4 zeolite catalysts remarkably enhanced the HDS activity. Introduction of the Mo3NiS4 core into zeolite as a precursor resulted in catalysts with higher HDS activity than that of Mo3S4 core and Ni2+ independently; it is conceivable that the intimate interaction between nickel and molybdenum in the precursor is effective at producing active species.