Freshwater snails of the genus Bulinus O. F. Müller, 1781 are intermediate hosts for schistosomes, trematode parasites which cause schistosomiasis. The genus includes closely related species complexes with restricted gene flow between populations of each taxon. Despite their importance as intermediate hosts, unambiguous identification of these snails remains challenging. We applied molecular approach to their identification to achieve a better understanding of the epidemiology of schistosomiasis in an endemic region, south-western Nigeria. A total of 149 snails were collected and their genomic DNA was screened for schistosome infection using PCR amplification of schistosome DraI repeat sequence. The snails were identified by PCR-RFLP and/or sequencing of an amplicon of their entire ITS region including the 5.8S ribosomal RNA (rRNA) gene. Four Bulinus species, namely B. globosus (Morelet, 1866), B. forskalii (Ehrenberg, 1831), B. camerunensis Mandahl-Barth, 1957 and B. senegalensis O. F. Müller, 1781 were identified, and 34.9% (n = 52) of the 149 snails were infected: B. globosus 25.5% (n = 38), B. forskalii 5.4% (n = 8), B. camerunensis 2.7% (n = 4) and B. senegalensis 1.3% (n = 2). Restriction fragment profiles of the ribosomal ITS region for B. globosus closely matched those obtained in our previous study thus confirming the view that ribosomal ITS region of these snails could be well suited for taxonomic studies. The use of sequencing for species identification was costly and time-consuming, but it was effective in resolving true identities of snails whose restriction profiles were similar and inconclusive.