A case of hermaphrodism in a wild Pacific bluefin tuna Thunnus orientalis from the Sea of Japan is reported. Morphologically and macroscopically, the gonad seemed to have both ovarian and testicular surfaces. Histological analysis showed that the gonad consisted of only sexually mature testis in all the sections examined, suggesting that the individual was male. Genetic analysis, however, indicated that the tissue samples from this individual had no male-specific genome region, resulting in it being inferred as a female. The observed inconsistency between genetic and histological analysis could help future understanding of the sex development of tunas.