To clarify population structure of finless porpoises (Neophocaena phocaenoides) in Japan, we examined mitochondrial DNA sequences of 174 animals. All individuals except for a female were collected in 5 geographically discrete coastal waters where Japanese porpoises are mainly distributed: Sendai Bay–Tokyo Bay, Ise–Mikawa Bays, Inland Sea–Hibiki Nada, Omura Bay, and Ariake Sound–Tachibana Bay. We analyzed 345 base pairs of the control region for all animals and detected 10 haplotypes. Two of those were shared by animals from > 1 area, whereas the other 8 were each found only in 1 area. The most common haplotype in Ise–Mikawa Bays and Ariake Sound–Tachibana Bay was not found at other locations. Analysis of the frequency distribution of haplotypes quantified genetic differentiation, and measurements of gene flow indicated limited dispersal of animals among locations. We conclude that finless porpoises in each of the 5 locations belong to distinct populations.