Previous study using the traditional method of screening snails for infection reported shedding of Schistosoma cercaria by Biomphalaria snails from a river in Nkalagu, southeastern Nigeria. This is contrary to published reports that Biomphalaria from this part of the country does not shed schistosome cercaria. Here, we employed the use of polymerase chain reaction (PCR) methods to screen and characterize the Biomphalaria snails from Nkalagu. Snails were collected from the River Uzuru in dry season, identified and subjected to molecular assays. Genomic DNA (gDNA) was extracted from whole tissues of the 212 Biomphalaria snails and amplified using conventional PCR to check for the schistosome infection level. Assay for the detection of S. mansoni infection was further done using a nested PCR (nPCR). We amplified the entire internal transcribed spacer 2 (ITS2) regions from gDNA of the 212 snails. The representative samples were sequenced and subjected to Blast searches to confirm snail species. Of the 212 snails screened, 164 (77.4%) of the snails were infected with schistosomes, but only 16 (9.76%) of the snails was positive for S. mansoni infection. Amplification of the snails' ITS2 region yielded a product of 460bp. PCR amplicons of eight of the snails infected with S. mansoni were selected for sequencing, and Blast searches confirmed the snails to be B. pfeifferi. The results show the presence of S. mansoni positive B. pfeifferi in Nkalagu and suggest there may be cases of intestinal schistosomiasis in this part of Nigeria soon.