The phylogenetic relationship between Margaritifera togakushiensis Kondo & Kobayashi, 2005, a newly recognised species distributed in the Japanese archipelago, and its closely related species, M. laevis (Haas, 1910) widely distributed in the same area, was analysed based on the mitochondrial COI and nuclear ribosomal (18S rRNA, 28S rRNA) gene sequences. The sequence data of several margaritiferids registered in GenBank were also used in the analysis. Margaritifera togakushiensis and the North American species M. marrianae were the most closely related species, forming a clade with which the Japanese M. laevis and the North American M. falcata were sisters. The two Japanese and two North American margaritiferid species, which occur on opposite sides of the Pacific Ocean, form the newest lineage in the Margaritiferidae, a family thought to be the most primitive of the freshwater pearl mussels, originating in the Mesozoic. Our results also support recent suggestions that generic names Dahurinaia and Cumberla...