Technical Abstract: There are 80 genotypes of Enterocytozoon bieneusi reported to infect humans, domesticated and wild mammals, and birds. Many molecularly similar genotypes cluster with specific host species and appear to be host specific such as the bovine isolates BEB1, 2, 3, 4, and 6. Others have been reported from infections in a variety of host species. For example, genotype D has been reported from humans in Germany, the United Kingdom, the United States, Peru, Gabon, Niger, the Cameroons, and Thailand, as well as from pigs, cats, macaques, muskrats, raccoons, beavers and foxes. Because genotypes are simply names that refer to gene sequences, they have no taxonomic status and do not follow any of the rules of the ICZN regarding species or other taxon naming. The present plethora of naming schemes has resulted in multiple names for the same genotype. Some genotypes have received 4, 5, or 6 names, each in a separate publication by different authors. For example, genotype D also has been reported as genotype pigEBITS9, WL8, and Peru 9. Even Microsporidia specialists find the names confusing and have difficulty in efficiently using the scientific literature. We propose a logical method for assigning names for the present and future genotypes that will be followed by investigators in this field, resulting in a system of names that can be clearly understood and will prevent further confusion.