We report a rare case of a deep stromal keratitis with a chronic indolent course, diagnosed as microsporidial keratitis from corneal scrapings. The patient's condition worsened despite medical therapy and penetrating keratoplasty was performed. The histopathology of the corneal tissue revealed multiple microsporidial spores in the posterior stroma and the endothelial exudates, whereas there was no clinical or histopathological breach in Descemet's membrane. This is the second report in the literature to report that micropsoridial spores can cross the intact Descemet's membrane.