Schistosomiasis is one of the world's most important parasitic infections. Its elimination has proved difficult even in countries such as Brazil where access to treatment is readily available. Infection is the result of human contact with surface water where there are infected snails, so that human biology and habits may bring different individuals in contact with different groups of parasites. Identification of schistosome subpopulations may assist understanding transmission patterns and guide control efforts. We compared microsatellite allele frequencies from all of the infections in 2 small villages and determined that the movement of parasites between them was limited. Individual infections were distinct composites of parasites, but if infected humans were grouped by demographic and epidemiologic characteristics, there was no evidence that specific parasite subpopulations were being selected in these types of hosts. Infections were also not differentiated when stratified by host's age indicating that the populations were stable over time. Since the infection cycle requires human fecal contamination of water, local human behavior can to some degree be inferred from the patterns of schistosome subpopulation distribution.