We investigated the genetic structure of populations of the brackish-water crab Deiratonotus cristatus (de Man, 1895) (family Camptandriidae) on the Japanese coast, together with morphological and the ecological variations. Genetic characteristics of the local populations based on mitochondrial DNA COI sequence data have revealed genetic differentiation between many populations, with the haplotype networks forming three geographical clades: a clade occurring on the Pacific coast, one occurring predominantly in northern Hokkaido, Kyushu and the Seto Inland Sea, and a third occurring in the Ryukyu Islands. Male pleopod morphology, carapace length relative to carapace width, and carapace width of adult crabs varied inconsistently among the geographic groups corresponding to the three clades. Life history traits were similar throughout, although differences in the breeding season were apparent between populations on the Pacific coast, and in the Seto Inland Sea and the Ryukyu Islands.