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Recently, synonymizing Eisenia with Ecklonia was suggested based on a molecular phylogeny using the rbcL gene and ITS1–5.8S rDNA sequences. However, in a multigene molecular phylogeny based on mitochondrial cox1, cox3 genes and the atp8–16S rDNA region, as well as the plastid atpB, psaA, psbA and rbcL genes, Ecklonia spp. formed a monophyletic clade supported by high statistical values, and Eisenia spp. showed monophyly depending on analytical methods. The Japanese Eisenia species that used to be identified as Eisenia arborea (E. arborea sensu Arasaki) was shown to be genetically distant from E. arborea from the NE Pacific and E. bicyclis from Japan. Eisenia spp. were morphologically distinct in having a split meristematic zone in the mature thallus forming a dorsi-ventral blade with false branches. Therefore, we propose reinstatement of Eisenia as an independent genus and describe a new species, Eisenia nipponica (= E. arborea sensu Arasaki) from Japan. E. nipponica is distributed on the Pacific Coast of central Honshu, having a separate geographic range from E. bicyclis, which is distributed on the Pacific coast of eastern Honshu and the Sea of Japan coast of north-western Honshu and northern Kyushu. [ABSTRACT FROM AUTHOR]