We report molecular orbital calculations (CNDO) of the desulfurization reaction of thiophene over a molybdena catalyst. In particular, we have studied the relative stabilities of several molybdenum oxide structures ranging from MoO to a linear chain Mo3O10. The processes of hydrogenation and sulfidation of Mo3O10 leading to vacancy formation were investigated. It was found that the formation of a partially sulfided active catalyst structure with a vacancy over the Mo atom was energetically allowed. Concerning the adsorption of thiophene on this catalyst model, our calculations show, however, that the CS bond cleavage need not occur prior to ring hydrogenation and that a concurrent hydrogenation of the β carbons may also occur quite readily. Finally, the role of cobalt as a vacancy stabilizer is also discussed.