Environmental pollution with human and domestic-animal fecal material is recognized as a potential pathogen pathway for wildlife infections with zooanthropomorphic protozoan parasites such as Giardia and Cryptosporidium. In this article, we review current knowledge about the diversity of free-living and captive terrestrial and marine mammalian wildlife species infected with Giardia and Cryptosporidium. The combination of prevalence studies with modern molecular-genotyping techniques is providing valuable insights into the host specificity and possible transmission routes of these two important parasites.