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Ilyoplax pusilla (De Haan, 1835), a Japanese intertidal mudflat inhabitant, is known to exhibit genetic differentiation between populations from mainland Japan and Ryukyu Islands. Morphological variation of I. pusilla was examined for possible correlations with the genetic population structure. Among adult specimens collected from four mainland and two Ryukyu Islands populations, two morphological types were found in each of three characters, i.e. abdominal telson of both sexes and male first pleopod, among which the variation of the male first pleopod was consistent with their respective population groups, which indicates a relationship between morphological variation and genetic differences.