Morphological characteristics of fossil bagrid catfishes from six Miocene to Pleistocene localities in Japan are described. A new species of the Middle Miocene bagrid,Pseudobagrus ikiensis, is described, based on five nearly complete specimens (ca. 19 cm SL) and one half-body specimen from the Chojabaru Formation (15 Ma) of the Iki Group in Nagasaki Prefecture. The species is diagnosed by a unique combination of characters: 14–16 anal fin rays, 44–47 vertebrae, deeply forked caudal fin, pectoral spines with serrations on the anterior edge and supraoccipital process extending to the first pterygiophore of the dorsal fin.Pseudobagrus ikiensis is morphologically close to the extantP. fulvidraco, which is widely distributed in China, Siberia and the Korean Peninsula, suggesting that both lineages had appeared by the Middle Miocene. All other fossil specimens are from the Pliocene (3–4 Ma) Ueno Formation (lowest Kobiwako Group, Ohyamada, Mie Pref.) and Tokai Group (Tsu, Mie Pref.), and Pleistocene cave deposits (Inasa, Shizuoka Pref., Mine, Yamaguchi Pref. and Kanogawa, Ehime Pref.). These are incomplete, comprising mainly dorsal and pectoral spines. Being indistinguishable from the extantP. nudiceps, they are thus considered to be included in that lineage. Although the geological distribution of these Plio-Pleistocene fossils nearly overlaps that of the extantP. nudiceps (west of the Suzuka Mountains), fossil specimens have also been found in the Ise Bay area (Tsu), whereP. ichikawai is the only extant bagrid, and further east (Inasa). Based on evidence that the latter is not a sister species ofP. nudiceps, the distribution of the fossils indicates that the range ofP. nudiceps was restricted to west of the Suzuka Mts. during the Pleistocene or Holocene.