We investigated geographic, genetic, and morphological variations in the intertidal limpet Lottia dorsuosa, a species with a broad distribution across Japan. A total of 98 specimens were obtained from 36 locations spanning the entire Japanese Archipelago, encompassing both the northern and southern regions. Examination of mitochondrial COI sequences revealed a distinct geographic genetic structure, delineating three prominent clades: (1) the Kuroshio Current, (2) the Tsushima Current, and (3) the Ryukyu-China groups. The observed geographical structuring between the Pacific and Sea of Japan side mirror patterns was noted in previously studied species, such as Turbo sazae and Batillaria attramentaria. Within L. dorsuosa, the Kuroshio Current group exhibited a substantial genetic distance, reaching a maximum of 12.35%, when compared to the more closely linked Tsushima Current and Ryukyu-China groups. Compared to other groups, the Ryukyu and China groups represented relatively recent differentiations, and the former group is currently facing a heightened risk of extinction owing to its sparse population density. The emergence of intraspecific geographic structures is likely attributable to the comparatively brief planktonic larval stage, which is a common characteristic of patellogastropod limpets.