Isanacetus laticephalus is a species of archaic baleen whales, that played a key role to recognize a problematic taxonomic confusion in so-called “cetotheres” for some time. HMG-1475 includes the posterior part of the skull and atlas, which was discovered from Biratori Town, Hokkaido, Japan. Radiolarian fossils suggest that HMG-1475 is late Burdigalian to early Langhian (16.7 to 15.3 Ma) in age. Here, we identify the specimen as aff. Isanacetus laticephalus, because HMG-1475 shares same conditions with Isanacetus laticephalus such having the sagittal crest at the vertex, narrower posterior ends of the premaxillae and nasals, posteriorly gradually converged middle part of the lateral borders of the nasals, anteriorly excavated and rounded border of maxillae at the vertex in dorsal view, and posteriorly well projected paroccipital process in dorsal view. HMG-1475 differs from I. laticephalus by having a distinct temporal crest and a more robust nasal. In Hokkaido, Taikicetus inouei was reported from the Middle Miocene, which is closely related to I. laticephalus. However, HMG-1475 differs from T. inouei by having a sagittal crest between the nasals and supraoccipital, and the temporal crest. HMG-1475 lacks the ear bones and was incompletely preserved. However, it implies that there was an unknown species similar to I. laticephalus around at Hokkaido, Japan (late Early to early Middle Miocene).