Genetic variation among temporally and spatially defined populations of the schistosome intermediate host, Biomphalaria pfeifferi, was analysed using RAPD markers. Snails were collected from each of eight sites that were 1-20 km apart, on four occasions, over a 2-year period. High levels of genetic variability were found within populations, between populations and between collections. Spatial differentiation and intrapopulation similarity were highest during periods of drought and were lowest following heavy rainfall. Temporal variability, consistent with founder effects, genetic drift and/or differential parasite pressure, was of similar or greater magnitude to that of the spatial variability. The results not only demonstrate that spatio-temporal sampling is necessary to understand the population genetics of short-lived species in variable habitats, but also provide empirical data to support current theoretical models of host-parasite co-evolution.