In Zanzibar, the freshwater hermaphroditic snail Bulinus globosus is the intermediate host of the human parasite Schistosoma haematobium. To shed light on the patterns of genetic variation within Bu. globosus, variation at six polymorphic microsatellite loci was assessed to quantify spatial genetic structure within eight populations and temporal changes in a further four populations of the snails. Limited genetic variation was observed within populations, possibly reflecting both partial-selfing and fluctuations in population size. Although a statistically significant heterozygote deficiency was observed, Bu. globosus appears to be a preferential out-crosser, which was consistent with the absence of genotypic linkage disequilibria. Genetic variation across populations was substantial, illustrating significant isolation-by-distance on a regional scale and that gene flow was restricted to nearby populations. The temporal survey showed that levels of genetic variation and inbreeding changed over a 1-year period, consistent with field observations of seasonal change. The results strongly support a snail demographic model of population expansion and contraction throughout the year with habitats re-colonized by aestivating or surviving snails from local refugia. This model might help explain co-evolution of snails and schistosomes in Zanzibar as local populations of Bu. globosus have varying degrees of susceptibility to S. haematobium.