Sulfur compounds in deep hydrodesulfurization (HDS)-derived diesels were effectively separated into thiophenic and sulfidic fractions using the methylation/demethylation method and characterized by gas chromatography-mass spectrometry (GC MS) and GC-sulfur chemiluminescence detector (SCD). Sulfidic fractions account for over 15 wt % of total residual sulfur, in which a series of refractory cyclic sulfidic compounds, 1,1-dimethylhexahydrodibenzothiophenes (1,1-DMH6DBTs) and 1,9b-dimethylhexahydrodibenzothiophenes (1,9b-DMH6DBTs), were found in the diesels, and larger molecular weight homologues were identified. Some homologue series of C-1-C-4 alkyl-substituted thiaadarnantanes were detected in the HDS diesel. These cyclic sulfidic components are refractory to deep HDS, which require more prudent catalysis and reaction systems to achieve ultralow-sulfur diesel (ULSD) production.