The nature and extent of genetic variation in Giardia was used to infer its mode of reproduction, population structure, taxonomy, and zoonotic potential. Ninety-seven isolates of Giardia duodenalis, from a defined area in Western Australia and throughout Australia and overseas, were obtained from humans, cats, cattle, sheep, dogs, goat, beaver, and rats. Enzyme electrophoresis revealed extensive genetic variation with 47 different zymodemes. The widespread occurrence of certain zymodemes and the similarity of relationships among isolates inferred from independent genetic markers suggests a clonal population structure for G. duodenalis, although occasional bouts of genetic exchange may occur. The 47 zymodemes clustered similarly in phenetic (UPGMA) and phylogenetic (Fitch-Margoliash) analyses. The level of genetic diversity in isolates from a defined geographical area in Western Australia was similar to the level of diversity in isolates from throughout Australia. These data suggest that clonal lineages within G. duodenalis are evolutionarily independent. Although there was a significant overall correlation between genetic distance separating zymodemes and occurrence in different host species, we found genetically identical isolates from humans and other animals and extensive genetic diversity between isolates from humans. We interpret this as evidence for zoonotic transmission of the parasite.