An annotated checklist of the marine fishes of the Hibiki-nada Sea and Mi-shima island, Yamaguchi Prefecture, Japan, was compiled on the basis of 382 specimens. A total of 70 families, 126 genera, and 154 species (105 species in Hibiki-nada Sea, 72 species in Mi-shima island) were listed in this study. Hemitrygon laevigata (Dasyatidae), Cypselurus spilonotopterus (Exocoetidae), Platycephalus sp. 1 (Platycephalidae) (called “Yoshinogochi” in Japan), and Parupeneus biaculeatus (Mullidae) represent the first records from the Sea of Japan.