Although relatively uncommon, fungi, atypical Mycobacteria, and Nocardia have been isolated from a variety of infections of eye including keratitis, scleritis, canaliculitis, dacryocystitis, endophthalmitis and orbital cellulites. The organisms typically cause a slowly progressive disease. The diseases caused by the organisms can pose both diagnostic and therapeutic challenges. In this manuscript we will describe updates on important aspects of the ocular infections caused by these organisms.