The catalytic activities of NiMo/Al2O3 and CoMo/Al2O3 with a variable content of Ni and Co, respectively, were examined for the hydrodesulfurization (HDS) of refractory sulfur species, 4,6-dimethyldibenzothiophene (4,6-DMDBT), in decane with naphthalene. Naphthalene of 10 wt.-% severely retarded the HDS of 4,6-DMDBT over the series of NiMo catalysts. Hydrogenation of naphthalene dominated over the series of NiMo catalysts, suppressing the HDS of 4,6-DMDBT over the catalysts. CoMo catalysts were superior to the NiMo catalysts for the HDS activities of 4,6-DMDBT with less retardation of the aromatic partner, providing the highest activity at Co content of 1 wt.-% in 15 wt.-% of Mo, although the former catalysts were inferior to the latter ones for the hydrogenation activities of the aromatic partner. The valence states of metals were observed by X-ray photoelectron spectra (XPS) to discuss the active sites for the hydrogenation especially selective to the sulfur species.