A Japanese small salamander, Hynobius naevius (Temminck and Schlegel, 1838), has recently proven to include two species (larger [A] and smaller [B]) that are reproductively isolated and are genetically and morphologically distinct from each other. Of these two species, Species A is considered to correspond to true H. naevius. To determine the name of Species B, we investigated five specimens stored at Kyushu University and concluded from the locality and date of collection that they represent syntypes of H. n. yatsui Oyama, 1947. Results of morphological comparisons indicated that the syntypes are identical with Species B. Because this species is distinct from Hynobius naevius at the species level, subspecies H. n. yatsui is elevated to full species rank as H. yatsui. To avoid taxonomic confusion, we designated one male among the syntypes as the lectotype and redescribed the species.