A new species of amphipod, Sternomoera morinoi Tomikawa and Ishimaru, is described from subterranean aquatic habitats in Shiga Prefecture, Japan. In addition, Relictomoera tsushimana (Uéno, 1971) from a well on the island of Tsushima in Japan is transferred to Sternomoera and redescribed based on the holotype. Sternomoera morinoi sp. nov. is most similar to S. tsushimana (Uéno, 1971) comb, nov., but is distinguished by having many fine setae on the body, a shorter antenna 1, fewer C-setae on mandibular palp article 3, a shorter mandibular palp article 3, sparsely setose anterior margins of coxae 1–4, a different armature of the palmar margins of gnathopods 1 and 2, and no long setae on the posterior margin of the basis in gnathopod 2 and pereopods 3 and 4. The phylogenetic relationships among the Japanese species of Sternomoera are also estimated, based on partial DNA sequences of the nuclear 28S rRNA gene.