Individuals of the brackish water ostracod species Ishizakiella ryukyuensis are found sympatrically with those of the closely related species I. miurensis at the Kii Peninsula, western Japan, and possess a projection on the male copulatory duct. By contrast, individuals of this species recovered from the Nansei Islands, southern Japan, do not have such a projection. Molecular phylogenetic trees based on mitochondrial COI sequences consistently indicated that the populations at the Nansei Islands formed a paraphyletic group outside of a cluster consisting of the population at the Kii Peninsula. Thus, the development of the projection in the male copulatory organ is considered as a derived character for the individuals at the Kii Peninsula, and this feature may have been brought about by the sympatric distribution and a process of character displacement.