The first osteichthyan fish fossil from Japan was described by D. S. Jordan in 1919. It is Iquius nippnicus from Iki Island, Nagasaki Prefecture. Fish fossils described for the first time by a Japanese researcher were Clupea tanegashimaensis and Percichthys chibei from the Pleistocene Tanegashima Island, Kagoshima Prefecture by S. Saheki in 1929. By 1994, about 28 species of ray-finned fish fossils from Japan were described, and the number has increased to 68 by 2018. Some major fish fossil assemblages have been found in Japan. The Wakino fish fauna from the Early Cretaceous lacustrine deposits in Kyushu consisted of three different fish faunae including 21 species, whereas the Tetori fish assemblage from the Cretaceous freshwater deposits in Ishikawa, Gifu and Fukui prefectures composed of five or six fishes including two described species. The Miocene Tottori marine fish assemblage consisted of many shallow water species including seven described species, and the Miocene freshwater fish assemblage recognized 15 species including described four species from Iki Island in Nagasaki Prefecture. The Pleistocene freshwater fish assemblage consisted of six species from Kusu Basin in Oita Prefecture, and the Pleistocene marine fish assemblage recognized more than 20 species from Tanegashima in Kagoshima Prefecture. Some specimens of each fish fossil assemblage have been studied and described, but the rest of the specimens are still waiting for further research. Each fish fossil group has sufficient potential of PhD projects, and not only the phylogenetic research of each taxonomic group but also the Mesozoic freshwater fish assemblages have the possibility to elucidate the relationship between Japan and the Eurasian continent and their biogeographic studies, and Cenozoic fish fossils have the potential to elucidate the origins and transitions of East Asian freshwater fish fauna including Japan and origins and transitions of Recent fish fauna in the western North Pacific Ocean.