We investigated genetic diversity and population structure of Sitka Periwinkle, Littorina sitkana in eastern Hokkaido, Japan, and found that the Shiretoko Peninsula is significant to maintain genetic diversity of this abundant and common species. Using partial sequences of mitochondrial cytochrome-b gene, 26 haplotypes were identified in 654 individuals. Haplotype distribution showed spatial structure, and restricted gene flow between local populations was indicated by significant FST values in almost all pairs of localities and significant isolation by distance. Haplotype and nucleotide diversities were much higher in examined samples than in northeastern Pacific populations, of which genetic diversity and population structure were previously reported, and especially higher along Shiretoko than the other coasts along eastern Hokkaido. The most abundant haplotype in northeastern Pacific was identical to a haplotype occurring in Shretoko. The present study revealed the significance of the Shiretoko Peninsula in coastal biodiversity of eastern Hokkaido and potential of L. sitkana as a model of genetic survey of littoral ecosystems in conservation area, though this species itself is not under the urgent issue of conservation.