Hydrodesulfurization (HDS) reactivity of a refractory sulfur species, 4,6-dimethyldibenzothiophene (4,6-DMDBT), was examined over a Y-zeolite containing CoMo/Al2O3 (CoMo/Al2O3-zeolite), conventional CoMo/Al2O3, and NiMo/Al2O3. Isomerization and considerable transalkylation of 4,6-DMDBT into 3,6-DMDBT and into tri- or tetramethyldibenzothiophenes, respectively, were observed characteristically over CoMo/Al2O3-zeolite catalyst. Migration of methyl groups enhances the HDS reactivity of the refractory sulfur species by diminishing the steric hindrance. Among the catalysts examined, CoMo/Al2O3-zeolite exhibited the best activity for HDS of the gas oil through the effective desulfurization of refractory alkyldibenzothiophenes.