The Sakura shrimp Sergia lucens is a remarkable meso-pelagic crustacean species, which is harvested for human consumption in restricted geographical areas of Taiwan and Japan in the northwestern Pacific. Nucleotide sequence analysis of the mitochondrial DNA control region was conducted to investigate the levels of genetic variability and differentiation between Japanese and Taiwanese populations of S. lucens. The latter half of the control region, which contained 589 nucleotide sites, was sequenced using DNA extracted from 178 individuals from the two geographical regions. Analyses yielded 162 haplotypes, and the amount of genetic variability within the populations as shown by the levels of haplotype and nucleotide diversity revealed that the two populations included in this study have higher levels of diversity than intraspecific variation previously reported in other crustaceans. Our AMOVA and pairwise Fst results indicated the existence of significant genetic differences between the Japanese and Taiwanese populations. Morphological analyses also revealed minor but notable differences between the two groups. These findings suggest that postulated gene flow of S. lucens is unlikely to occur across the isolated Japanese and Taiwanese populations, and that each population completes their life history in a restricted geographical area.