Long distance dispersal (LDD) from the mainland to an island is a rare event, having been regarded as distinct from short distance dispersal (SDD) within an island. Here, we dealt with population genetics of Gyraulus freshwater snail on oceanic Chichijima Island using genome-wide single nucleotide polymorphisms obtained from MIG-seq method by second generation sequencer. As a results, the analyses showed that snail had clear geological differentiation without current gene flow within the small island in spite of short distance isolation after it had colonized from remote source region via long distance dispersal over 1000 km. Within the island, it is presumed that rare short distance dispersal had caused current differentiation and geographical pattern, and these suggested rare chance dispersal was an essential driver of constituting biological diversity. Our results showed that SDD could also be a rare chance event similar to LDD in organisms with low active dispersal.