The Japanese Archipelago harbours high diversity of endemic bradybaenid land snails. However, there have been few systematic studies of these snails. The resolution of the taxonomy and phylogenetic relationships of these bradybaenid land snail taxa is important both for describing species diversity and for promoting the conservation of these land snails. We investigated the molecular phylogeny of Bradybaena and Phaeohelix using the CO1 and internal transcribed spacer genes, to clarify whether morphological traits and the current species taxonomy of these genera reflect their phylogenetic relationships. Our results show that the Japanese species in these genera are genetically divided into three clades, and the geographical distribution pattern of the lineages tends to reflect phylogenetic relationships. Although the nominal species taxonomy of these genera was not consistent with their molecular phylogenetic relationships, their shell and genital morphology reflected phylogenetic relationships to some extent. Inferred phylogeny and observed genital morphology showed that Phaeohelix submandarina, P. miyakejimana and Bradybaena circulus oceanica from Hachijo-kojima Island belong to P. phaeogramma. In addition, the distinction between Bradybaena and Phaeohelix was not supported by molecular phylogeny, showing instead that Phaeohelix should be synonymized with Bradybaena. This study suggests that a further taxonomic revision of Japanese Bradybaenidae is needed and, to address this issue, genital anatomy is useful in addition to molecular phylogenetic analyses.