Although marine phylogeographers have accumulated knowledge of the evolutionary history of various invertebrates, there is a large bias among the taxa regarding genetic data. The order Polycladida is a typical example for which little genetic information at population level is available. Here, we focused on the polyclad flatworm Stylochoplana pusilla, distributed in the Japanese Pacific coastal area. Stylochoplana pusilla is known to have commensal relationships with certain intertidal snails, using snails (mainly Monodonta confusa) as a refugee house. During low tide, S. pusilla hides in the mantle cavity of snails to protect themselves from desiccation and predation. Here, we investigated the genetic structure of S. pusilla using a mitochondrial Cytochrome Oxidase I marker and the species diversity of snails used by it. We found that S. pusilla has high genetic diversity of its populations. While S. pusilla showed a significant genetic differentiation among populations, it was relatively low. In addition, we also showed that S. pusilla used several intertidal snail species which inhabit various coastal environments. The present study suggests S. pusilla has sufficient dispersal ability to connect among its local populations. Also, the range of available snails for S. pusilla may help the connectivity among local populations. We provide important knowledge about this invertebrate taxon with a unique ecology, which has been insufficiently studied.