Dytiscus sharpi is a critically endangered diving beetle endemic to Japan that is distributed in five distant areas today. Information on the population genetics of this species is crucial for its conservation. We investigated the genetic differentiation and divergence of the D. sharpi in seven populations in North and South Hokuriku on the Sea of Japan side, using mitochondrial cytochrome oxidase subunit I (COI) and nuclear Histone 3 and 28S rRNA gene sequences. Although the nuclear markers showed little geographic genetic differentiation, nine COI haplotypes were identified from 31 individuals, and these haplotypes were divided into two distinct networks A and B. The network A consisted of a single haplotype, and network B consisted of eight haplotypes. The populations in North Hokuriku possessed the haplotypes of both networks, whereas those in South Hokuriku possessed only the haplotypes of network B. The genetic diversity was relatively high in South and North Hokuriku. However, populations in South Hokuriku showed low genetic diversity and the isolation-by-distance pattern was observed among the populations, suggesting a restricted gene flow. Phylogenetic analysis including the data from a previous study revealed that the network A was closely related to a haplotype from Kanto, which is on the Pacific side. These results suggested that in the past this species was distributed widely across the Hokuriku area and the fragmentation of its distribution areas is a recent event. These results will contribute to strategies for the preservation of the current genetic diversity of D. sharpi.