Elaphognathia cornigera is a sponge-dwelling species of isopod that occurs in the intertidal zone in the main island of Japan. Currently, another population of Elaphognathia has been found from Okinawa-jima Island (classified as Elaphognathia sp.). Although it is quite similar in morphology to E. cornigera, the habitat and seasonal traits are quite different between Okinawa-jima Is. and Izu Peninsula. In this paper, we examined Elaphognathia sp. and E. cornigera from several sampling sites using morphological analysis and ribosomal DNA ITS2 sequences. Morphological analysis revealed adult males of Elaphognathia sp. were distinguished from E. cornigera by the number of pylopod seta: E. nunomurai, 5.5 ± 1.1 (Haneji, N  =  18) and 4.1 ± 1.4 (Odo, N  =  18); E. cornigera, 11.6 ± 2.0 (Amakusa, N  =  18) and 13.7 ± 1.4 (Miura, N  =  18). Elaphognathia sp. were also distinguished from E. cornigera by means of rDNA ITS2 sequences, with differences between the E. cornigera group and Elaphognathia sp. being 5.3 and 5.9%, whereas the sequence differences between E. cornigera from Miura, Shimoda, and Amakusa were relatively low (0.5-1.4%). Thus, we describe a new species, Elaphognathia nunomurai.