A dibenzothiophene (DBT)-degrading bacterial strain was isolated from dyeing industry wastewater and identified as Nocardia sp. CYKS2. The newly isolated bacterial strain Nocardia sp. CYKS2 was able to convert DBT to 2-hydroxybiphenyl (2-HBP) as the dead-end metabolite through a sulfur-specific pathway. Other organic sulfur compounds, such as thiophene derivatives, thiazole derivatives, sulfides, and disulfides were also desulfurized by Nocardia sp. CYKS2. In batch culture, 0.2 mM DBT was completely desulfurized in 60 h. After DBT was depleted, neither cell growth nor 2-HBP production was observed. When a model oil which DBT was dissolved in hexadecane was treated with growing cells, DBT was desulfurized from 10 mM to about 2 mM in 80 h. In this case, desulfurization rate was 0.279 mg-sulfur/(L-dispersion.h), which was about 2.5 times higher than that in the previous case of batch culture. When diesel oil was treated, the sulfur content decreased from 0.3 to 0.24 wt % in 48 h. A volumetric phase ratio of oil to water was 1/10 in this case. The sulfur decreased from 0.3 to 0.2 wt % in 48 h, when the volumetric phase ratio was 1/20. The desulfurization rates were 0.909 and 0.992 mg-sulfur/(L-dispersion.h), respectively.