Marine organisms with a planktonic larval stage can passively disperse long distance and are thus expected to have a wider distribution range and lower geographic variation. However, recent molecular phylogenetic studies have revealed that they often display a clear geographic genetic structure or even form a geographically fragmented species complex. These genetic divergences can be facilitated by the presence of dispersal barriers such as oceanic currents and/or by the limitation of suitable habitats. Using comprehensive phylogenetic analyses, we evaluate how such dispersal barriers shape genetic divergence and speciation in the intertidal snail genus Monodonta. Our phylogenetic analysis revealed various patterns of cladogenesis in Monodonta in East Asia. Genetic segregation between the Japanese and Ryukyu Archipelagos are detected in M. labio and M. perplexa perplexa. However, the relationship of geographical border and lineages does not correspond to those two because they show different habitat preference. M. labio distributed in the Japanese mainland is separated by the boundary corresponding to the point from which oceanic currents split into different directions. In contrast, species inhabiting various environments such as M. confusa are not genetically separated in Japan. In the peripheral oceanic Ogasawara Islands, two Monodonta species form each endemic lineage, although these two underwent different colonization processes to the islands. These findings suggest that the genus Monodonta has been genetically diversified around Japan, probably due to its correlations with dispersal ability, oceanic current, and habitat preferences. These factors may be effective causes for diversification of marine gastropods with a planktonic stage.