Random amplified polymorphic DNA (RAPD) markers were used to assess distribution and genetic diversity of Schistosoma haematobium populations within their bulinid intermediate hosts in Mali. Naturally infected snails (Bulinus truncatus and B. globosus) were collected at four sites in the Bamako district. S. haematobium cercariae from single snails were used to infect mice and genotypes of the resultant adult worms were characterized using RAPD markers. Diversity indices were calculated at the scale of one snail, both within and among sites. One third of the molluscs harboured multiple miracidial infections (the maximum number equal to five) with slightly overdispersed distributions in three sites and a random distribution at one site. Similarity indices revealed significantly less variation among populations compared with populations, indicative of the absence of distinct S. haematobium populations within the Bamako district. RAPD markers represent an accurate tool for determining genetic diversity and amount of gene flow among parasite populations contained within different individual snails and among intermediate host populations.