The activities of molybdenum naphthenate and cobalt naphthenate for benzothiophene desulfurization are studied at 350 to 400°C and 6.9 to 13.8 MPa pressure. Molybdenum is found to be more active than cobalt naphthenate for desulfurization. At 400°C, using 104 mg/kg Mo on benzothiophene in tetralin under 6.9 MPa H2, over 90 mol % conversion of benzothiophene to ethylbenzene is observed. No styrene is detected. The dominant pathway for desulfurization is proposed to be via the initial hydrogenation to dihydrobenzothiophene, followed by elimination of H2S to generate ethylbenzene. The relative roles of donor solvent and molecular hydrogen in desulfurization are evaluated using a novel application of statistical analysis and fractional factorial design. At 4000 mg/kg Mo on benzothiophene, statistical analysis clearly isolates hydrogen atmosphere as the dominant factor affecting benzothiophene conversion. This result is also in agreement with thermodynamic predictions where benzothiophene conversion proceeds more favorably with hydrogen relative to tetralin.