Deep hydrodesulfurization (HDS) of diesel fuel oil was designed based on the recognition that alkyl dibenzothiophenes such as 4-methyl- and 4,6-dimethyldibenzothiophenes were the main target for deep HDS. Multi-stage and fractional HDS were very effective to achieve satisfactory HDS in terms of both sulfur level and fluorescent color of desulfurized oil. Catalysts with the selective hydrogenation of refractory sulfur species in major aromatic partners and isomerization-disproportionation of their alkyl groups prior to HDS were also designed to promote the desulfurization of such sulfur species.