In the late 1970s eight Balaenoptera specimens of unknown identity were caught in the lower latitudinal Indo-Pacific waters by Japanese research whaling vessels. The combination of the allozyme patterns and physical maturity of the eight specimens separated them from all acknowledged Balaenoptera species. In September 1998 we collected a medium-sized baleen whale carcass on a coastal island in the Sea of Japan. This specimen and the previously collected eight specimens resembled Balaenoptera physalus (fin whale) in external appearance but were much smaller. Comparison of external morphology, osteology and mitochondrial DNA data grouped the nine specimens as a single species but separated them from all known baleen whale species. Therefore, here we describe a new species of Balaenoptera, which is characterized by its unique cranial morphology, its small number of baleen plates, and by its distant molecular relationships with all of its congeners. Our analyses also separated Balaenoptera brydei (Bryde's whale) and Balaenoptera edeni (Eden's whale) into two distinct species, raising the number of known living Balaenoptera species to eight.