Molecular tools have greatly expanded our understanding of host parasite interactions, including pathogen / parasite diversity, host specificity and transmission pathways. This is particularly so for the protozoan parasites Cryptosporidium, Eimeria and Giardia, major causes of gastrointestinal disease in many vertebrate species. For Cryptosporidium 70% of the currently recognised species were described over the last 10 years and molecular data has been integral to these descriptions. Molecular analyses have also revealed greater than 40 cryptic Cryptosporidium species in diverse wildlife hosts, for which we have limited biological information. A similar pattern is also evident for Giardia. For Eimeria the application of molecular tools has not been as rapid, and much of our understanding of the diversity of Eimeria stems from morphological and pathological data. We have been using recent advances in molecular understanding of parasite diversity to investigate the application of multi-parasite targets and their interactions with endangered wildlife as a measure of human impacts. We show a significant association between parasite communities and proximity to humans, and a higher prevalence of parasites that commonly cause human infection in wildlife hosts. Our data demonstrates movement of parasitic protozoa at the interface between humans : domestic animals : wildlife and transmission of terrestrial parasites into marine ecosystems. I will discuss how the increasing knowledge of these parasites, in combination with other parasite targets, can be applied to investigate human impacts on host-parasite relationships in endangered species.