The brachiopod Lingula rostrum (Shaw, 1798) collected from Japanese waters was compared morphologically and phylogenetically in terms of shell morphology with L. anatina and L. reevii (Kuramochi et al, 2012). 18S rRNA gene sequences were also compared with other Lingula species. The specimens of L. rostrum, L. anatina, and L. reevii were collected from Seto Inland Sea (Off-Okayama, Bisanseto), Amami-Ohshima Island, and Ariake Sea, respectively, and used for comparison. The shell of L. rostrum was distinguished from L. anatina and L. reevii by allometric morphology and fresh tissue coloration. Based on the 18S rRNA gene sequences of L. rostrum along with those from L. anatina, L. reevii, and other species registered in a DNA database, a phylogenetic tree was constructed. The brachiopod L. rostrum was placed in a separate clade from other Lingula species, which suggests that L. rostrum should be regarded as non-closely related species.