To clarify phylogenetic relationships of Bryde's whales, we examined the nucleotide sequence of the mitochondrial control region and cytochrome b gene in 33 animals: 12 from offshore waters of the western North Pacific, five from off the Solomon Islands, and 16 from the East China Sea and coastal waters of Kochi in southwestern Japan. For reference purposes, homologous sequences from four Balaenoptera species including four Bryde's whales collected in the eastern Indian Ocean were added. We found whales from the three sampling areas to be genetically distinct. The control region sequences suggested that the whales from the three areas separate at higher than the populational level from one another. The cytochrome b data indicated that genetic differences between whales off the Solomon Islands and animals in the other two areas are equivalent to values found among recognized Balaenoptera species, although such a relationship was not observed between the other two areas. We conclude that whales in the East China Sea and coastal waters of Kochi separate from Bryde's whales in offshore waters of the western North Pacific at higher than the populational level but lower than the specific level (i. e., at the subspecific level) and that whales off the Solomon Islands do not belong genetically to the Bryde's whale as previously recognized.