Histological studies were carried out with 49 specimens; 18 Biomphalaria tenagophila guaibensis, 19 B. t. tenagophila and 12 B. occidentalis, collected in 10 municipalities in the states of São Paulo and Rio Grande do Sul, Brazil. The study considered histological aspects of the vagina, vaginal pouch and penial complex. In this study, we describe, for the first time, the histological features of the vagina, vaginal pouch and penial complex of B. t. tenagophila, B. t. guaibensis and B. occidentalis. The lining epithelial tissue and muscular tissue of the vagina, vaginal pouch and penial complex show a similar pattern in B. t. tenagophila, B. t. guaibensis and B. occidentalis, except for the intermediate muscular layer of the prepuce, which distinguishes B. t. guaibensis from the other two taxa. Histological studies on the penial complex and vagina region of other Biomphalaria species are necessary to confirm the taxonomic value of these two regions, in order to contribute to the group’s systematics.