To characterize the extent of genetic diversity of Schistosoma haematobium within and among its definitive host (intra- and interhost parasite diversity), 133 individual isolates from 25 infected schoolchildren were compared using randomly amplified polymorphic DNA markers. With 4 primers, 53 unambiguous loci were identified, and of these, 22 were polymorphic. Mean heterozygosity in the population was 0.116 ± 0.043. Analysis of molecular variance showed the majority of variance occurred within, rather than between, hosts. Frequencies of certain alleles segregated the parasite population into 13 distinct clusters of associated genotypes, with 4 of these first appearing 10 mo after the initial survey. Considering the level of diversity within this limited geographical area and the possibility of rapid turnover of genotypes, parasite variance may impact acquired immunity and clinical outcome of the infection.