A previous report on the B. pfeifferi snail found in Nkalagu, southeastern Nigeria, indicated that the snail does not shed Schistosoma cercaria. However, in a recent study, we discovered that the snail does shed Schistosoma cercaria, prompting an investigation into its phylogeny. This study aimed to trace the evolutionary history of B. pfeifferi from Nkalagu. We retrieved ITS2 sequence data from eight samples of Nkalagu B. pfeifferi from GenBank NCBI, along with sequences from B. pfeifferi found in other regions of Africa. Using MEGA 11, we constructed a phylogenetic tree and an evolutionary divergence matrix. The resulting tree revealed four clusters. Notably, B. pfeifferi sample 6 from Nkalagu showed a close relationship with B. pfeifferi samples from Yaoundé, Cameroon, and other African regions. In contrast, Nkalagu samples 1 and 4 exhibited a connection with another population of B. pfeifferi from a location in Cameroon that is not Yaoundé. Meanwhile, Nkalagu samples 2, 3, 5, 7, and 8 clustered together, displaying high evolutionary divergence from samples 1, 4, and 6, as well as from B. pfeifferi found in other parts of Africa. These results suggest the presence of B. pfeifferi with varying levels of genetic differentiation in Nkalagu.