Enterocytozoon bieneusi is emerging as an important cause of chronic diarrhoea in AIDS patients. Its reservoirs and transmission patterns are unknown. In this study, we have examined E. bieneusi sequences from four Rhesus macaques of different origin, which were kept at one animal facility. The sequences were identical in all animals, which suggested that infection had occurred within the facility. Full sequence agreement of E. bieneusi from macaques was found with an E. bieneusi genotype that occurs frequently in humans. To clarify, the relevance of possible inter-species transmission from man to macaque, a phylogenetic analysis was conducted including all sequences of E. bieneusi deposited in GenBank. The hitherto used system of diverse nomenclatures could be reduced to an outlier group and three main lineages, one of which could be further sub-divided into five subgroups. Based in this phylogeny, an association of parasites and host species could be observed for main lineages 2 and 3, as well as for most of the subgroups of main lineage 1. For confirmation, the phylogeny of main lineage 1 was reconstructed with an alternative method of distance estimation, yielding essentially the same parasite-host associations. Zoonotic potential of E. bieneusi is thus supported on a phylogenetic basis.