A new loach species, Misgurnus amamianus, is described based on 27 type specimens sampled from Ryukyu Islands, Japan. This new species can be distinguished from its congeners by the following combination of characteristics. 1) In adult males, a lamina circularis at the base of the pectoral fin is poleaxe-shaped and rounded at the back. 2) The last ray of dorsal fin is not branched, and its length is less than half the length of the second-branched soft ray. 3) The projected length from the posterior edge of the anal-fin base to the caudal-fin base is longer than the length from the insertion point of the pelvic fin to the anterior edge of the anal-fin base. 4) The ridges on the caudal peduncle at the upper and lower edges are weakly developed. The validity of this new species is also supported by the phylogenetic analysis of the mitochondrial DNA control region.