Single-strand conformation polymorphism (SSCP) analysis of the second internal transcribed spacer (ITS2) of nuclear ribosomal DNA provides a molecular tool for the identification of Schistosoma haematobium, Schistosoma guineensis and the hybrids of these two species. This molecular tool was utilized to provide a detailed analysis of the interactions between S. haematobium and S. guineensis in hybrid zones of Loum, Littoral Province, Cameroon. Individual hybrid schistosomes were identified within the natural populations collected from Loum in 1990, 1999 and 2000, which would have been misidentified as S. haematobium using solely morphological and sequence criteria. This study indicates the complexities of the hybridization between S. haematobium and S. guineensis and emphasizes the importance of assessing morphological, biological and molecular data to gain insights into the interaction of these two species over time.