The morphological and anatomical characters applied to determine species identity in the Bulinus africanus group species are insufficient to unambiguously discriminate between arbitrary species of given populations. In order to solve this problem, four snail populations from Kenya have been investigated morphologically and anatomically, and the species status compared with the result of molecular methods. We have amplified the entire ITS region and found that the investigated populations showed intra-specific genetic polymorphism, thereby giving the taxa an identity which were indistinct when the region was cut with restriction enzymes. Instead, an amplification of the sub-region ITS 1 revealed an unambiguous identification. because the amplification revealed only one single fragment. We also found that the observed heterogeneity of the entire ITS region could be confined to the sub-region ITS 2. Furthermore, the micro-sculpture of the shell and penis to preputium proportion, which are normally applied as morphological characters, might be considered as inadequate, because of the lack of a significant difference in those characters between the two well established species, namely B. africanus and B. nasutus in the Kisumu area. Instead, these two taxa were determined by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) to be one single species with a highly variable morphology. This result was further confirmed by random amplified polymorphic DNA (RAPD) data and the mitochondrial cytochome oxidase subunit I (COI).