| Organism | Nonhuman species | Disease | HIV | Non-HIV |
| Enterocytozooan bieneusi | Pigs, primates | Intestinal, hepatobiliary | + | + |
| Encephalitozooan intestinalis (Septata intestinalis) | Some mammals | Disseminated | + | +/- |
| Encephalitozooan hellem | Parakeets | Disseminated | + | - |
| Encephalitozooan cuniculi | Rabbits, mice, cats, foxes, dogs | Corneal stroma | + | + |
| Nosema connori | - | Disseminated | + | - |
| Nosema ocularum | - | Corneal stroma | + | + |
| Nosema-like species | - | Corneal stroma | + | + |
| Trachipleistophora hominis | - | Skeletal muscle, nasal sinuses | + | - |
| Trachipleistophora antropophtera | - | Disseminated | ||
| Pleistophora spp | Fish | Skeletal muscle | + | + |
| Vittaforma corneae (Nosema corneae) | - | Corneal stroma | + | + |
| Microsporidum spp (species not fully classified) | - | Disseminated |
