Hundreds of genera and thousands of species of obligate intracellular spore forming eukaryotes constitute the phylum Microspora. Currently these organisms are known to cause infections in the immunocompromised individuals in whom they exhibit diverse clinical manifestations including pulmonary, ocular, intestinal, muscular and renal disease. Ocular microsporidiosis can present as an isolated entity or as a part of systemic infection. Infection is acquired by traumatic inoculation or by contact with contaminated soil or water. Clinically this infection can present as stromal keratitis, scleritis, keratoconjuntivitis and endophthalmitis. Seven genera have been found to be associated with human ocular infections. Infections by these pathogenic organisms involve unique pathogenic mechanism- injection of the sporoplasm in the host cell via polar tube. Protean clinical manifestations and resemblance to herpetic keratitis poses as a challenge in clinical diagnosis of this condition. Diagnosis therefore mainly depends on morphological demonstration of these organisms. Electron microscopy is the ‘gold standard’ diagnostic method to detect microsporidial spores. Molecular methods like PCR, real time PCR are sensitive tests and aids in identification till the species level. Drugs like albendazole and fumagillin are widely used to treat microsporidial keratitis. Penetrating keratoplasty is useful in treating medically non responding cases.