Recent molecular ecological studies have focused on how the relationships between physical and ecological factors influence marine biogeography. Comparative phylogeography using closely related species is a powerful approach to evaluate the role of ecological traits in the genetic variation of marine organisms. In the present study, we compared ecological traits and genetic variation in 3 species of the intertidal snail genusMonodontathat co-occur in the Japanese and Ryukyu archipelagoes. We found thatM. labiowas dominant in sheltered habitats andM. perplexawas dominant in wave-exposed habitats, whileM. confusashowed no habitat specificity. This indicates thatM. labioandM. perplexaarehabitat specialists regarding wave exposure, whileM. confusais a generalist.M. labioandM. perplexashowed lower genetic diversity and greater genetic differentiation among populations thanM. confusa. Our findings support the specialist-generalist variation hypothesis in a well-connected marine environment.