Freshwater snails of the Bulinus forskalii group are one of four Bulinus species complexes responsible for the transmission of schistosomes in Africa and adjacent regions. The species status of these conchologically variable and widely distributed planorbids remains unclear, and parasite compatibility varies considerably amongst the eleven taxa defined, making unambiguous identification and differentiation important prerequisites for determining their distributions and evolutionary relationships. Random Amplified Polymorphic DNA (RAPD) analyses were used to investigate relationships between taxa, with particular emphasis on Central and West African representatives. RAPD-derived phylogenies were compared with those from other independent molecular markers, including partial sequences of mitochondrial cytochrome oxidase subunit I (COI) gene, and the nuclear ribosomal RNA internal transcribed spacer 1 region (ITS1). The phylogenetic reconstructions from the three approaches were essentially congruent, in that all methods of analysis gave unstable tree topologies or largely unresolved branches. There were large sequence divergence estimates between species, with few characters useful for determining relationships between species and limited within species differentiation. Nuclear and mtDNA sequence data from Central and East African representatives of the pan-African B. forskalii showed little evidence of geographical structuring. Despite the unresolved structure within the phylogenies, specimens from the same species clustered together indicating that all methods were capable of differentiating taxa but could not establish the inter-specific relationships with confidence. The limited genetic variation displayed by B. forskalii, and the evolution and speciose nature of the group, are discussed in the context of the increasingly arid climate of the late Miocene and early Pliocene of Africa.