In a recent review of the seagrass genus Halophila in Japan, eight taxa including four new species were listed: (i) H. decipiens , (ii) H. minor , (iii) H. major , (iv) H. ovalis , (v) H. mikii , (vi) H. nipponica , (vii) H. okinawensis , and (viii) H. gaudichaudii . In this study, the specific concept of Halophila in Japan as well as some other geographic areas was re-assessed by a combination of nuclear ribosomal ITS1, 5.8S rDNA, and ITS2 sequence analyses and morphological examinations of both recently collected materials and available type collections. The results confirm the distinctness of the Australian endemic species H. australis and the putative pan-tropical taxon H. decipiens ; but also demonstrate conspecificity of: (i) H. minor and H. ovalis ; (ii) H. major and H. mikii ; and (iii) H. nipponica , H. okinawensis and H. gaudichaudii . As an outcome of this study, we recommend restricting the list of Halophila representatives in Japan to the following four species: (i) H. decipiens , (ii) H. major , (iii) H. ovalis , and (iv) H. nipponica . In addition, we predict the possibility of H. major occurring further south than currently recorded.