The genus Encephalitozoon are spore-forming obligate intracellular microsporidian parasites that infect a wide range of organisms, including protists, invertebrates, humans, and many other vertebrates and known as opportunistic pathogen associated with immunocompromised individuals. Major symptoms include a life-threatening chronic diarrhea and systemic disease. The transmission routes may involve person-to-person as well as waterborne or foodborne, especially in developing countries with poor sanitation. E. intestinalis is recognized as one of the most frequently identified microsporidia in humans.