Morphological differences in microsculpture on the internal surface of penial tube are often useful to separate species but not genera or families in hermaphroditic snails. This suggests that penial sculpture has evolved rapidly relative to the other genital morphology, which could classify groups above the species level. At copulation, the internal surface of the penis is exposed inside out and attached to the partner's genital pore. Our previous studies exemplified that penial insertion is ceased without seminal transfer in mating between two congeneric species. This indicates that both or either one of the two species finally recognizes the other species at the stage of penial insertion after performing courtship. Thus penial sculpture may play a role for sexual isolation. The present study in two genera demonstrates that the morphology of penial sculpture detects interspecific divergence between taxa classified into subspecies based on shell morphology. We also found that premating isolation in sympatry is incomplete between species with little difference in penial sculpture, despite having been classified into different genera. Molecular phylogeny supported these findings.