Using samples from bycaught finless porpoises, cytochrome b sequences were analysed and phylogenetic trees were constructed. The aims were to: (1) determine genetic divergences within the genus Neophocaena; (2) examine interspecific divergences between N. asiaeorientalis and N. phocaenoides; and (3) examine intraspecific divergence between N.a. asiaeorientalis and N.a. sunameri. For this purpose, complete cytochrome b sequences for 12 N.a. sunameri specimens, collected from fishery markets at Pohang in southeastern Korea, were obtained, and these sequences were compared to the corresponding partial (402bp) and complete (1,140bp) sequences of Neophocaena, obtained from GenBank. From a maximum likelihood tree with the partial sequences of the two Neophocaena species, two clades were detected, corresponding to the two species, with average genetic distance of 1.64%, four fixed site differences (1.00%), and a Gst value of 0.64, although we did not examine the specimens from Southeast Asia and contiguous South China Sea. Furthermore, from the complete sequences, we recognised a lack of genetic divergence between the two subspecies of N. asiaeorientalis, with a Gst value of 0.06 and two pairs of identical sequences between them, indicating that our results do not support current subspecies classification. Thus, we newly found that our cytochrome b sequencing results are useful for the examination of interspecific and intraspecific divergences in Neohpocaena, although further genetic analyses with additional specimens of Neophocaena across its distributional range are necessary to confirm the findings in this study.