Interactions between schistosomes are complex with some different species being able to mate and hybridize. The epidemiology of schistosomiasis in specific areas of South West Cameroon has evolved remarkably over 30 years as a result of hybridization between Schistosoma guineensis and S. haematobium. Morphological and biological data suggest that S. haematobium replaced S. guineensis in areas of Cameroon through introgressive hybridization. Data are reported on the use of single stranded conformational polymorphism (SSCP) analysis of the nuclear ribosomal second internal transcribed spacer (ITS2) of individual schistosomes from hybrid zones of Cameroon. The data show that since 1990 S. haematobium has completely replaced S. guineensis in Loum, with S. haematobium and the recombinants still present in 2000. This study illustrates the complexities of the dynamics between S. haematobium and S. guineensis in South West Cameroon.