We document extensive incongruence between molecular phylogeny and the current taxonomy of the freshwater gastropod family Viviparidae in Japan. A phylogeny based on the mitochondrial cytochrome oxidase subunit I and 16S rRNA genes for East Asian viviparids comprises three major clades, the two largest of which are composed primarily of paraphyletic or highly polyphyletic taxonomic species. Sinotaia quadrata histrica includes several lineages whose geographical distribution and shell morphology are largely incongruent with their phylogenetic relationships. Several individuals identified as Heterogen longispira are nested within a clade of Cipangopaludina japonica. In contrast, Cipangopaludina chinensis laeta and C. c. chinensis from China are both monophyletic, but the two are not supported as sister taxa. The observed incongruence between phylogeny and taxonomy may be due to incomplete lineage sorting, introgressive hybridization and/or phenotypic plasticity. Further molecular phylogenetic analyses are needed to clarify the significance of the observed patterns and to verify the systematic relationships.