The morphology of non-genitalic structures in males is often associated with mating and courtship, and the evolution of those structures may cause speciation. In the present study, we describe a new species of marine interstitial ostracod from Japan. Morphological comparisons and molecular phylogenetic analysis based on ITS (internal transcribed spacer) 1 and ITS2 sequences revealed intraspecific variation on the male upper lip in the new species. The male upper lip of Parapolycope Klie, 1936 species has been reported to be related to mating behavior, and it likely produces species-specific stimuli for the female. The results of this study suggest that the male upper lip morphology in Parapolycope changed at the early stage of the speciation process.