A periwinkle, Littorina sitkana Philippi, 1846, does direct development and exhibits three types of shell sculpture. Lacking pelagic larval stages, this species is expected to be genetically differentiated among populations. In the present study, genetic variation of 19 populations along northern Japanese coasts was examined using protein electrophoresis. The relative abundance of shell types was also investigated at each locality. The analyzed populations were significantly differentiated genetically from one another. However, no significant genetic difference was detected between shell types within localities where two types were nearly equally frequent. When clustered genetically using UPGMA, the populations were divided into four geographic groups. The UPGMA tree also showed that the Japanese population of L. sitkana is clearly divided into two groups, which may have been derived from two mother populations with different genetic structures. On the other hand, allozymic and anatomical analyses of the present samples have refuted possible occurrence of sibling species of L. sitkana on the coasts of northern Japan.