We report two cases of Fusarium keratomycosis in which molecular analysis was used to identify two rare causative Fusarium species. A 65-year-old woman was diagnosed with Fusarium keratomycosis caused by F. equiseti, confirmed by sequencing the internal transcribed spacer (ITS) region and morphological characteristics. She was initially treated with topical corticosteroid but the keratitis did not improve. Even after aggressive antifungal treatment, there was a severe reduction of vision. In the end, the eye perforated. Our second case was a 75-year-old man who had diabetes mellitus. He developed keratitis after his cornea was injured by corn stalks. The ITS region identified the causative organism as F. verticillioides. Unlike the first case, he had good visual recovery after early antifungal therapy. Our findings demonstrate that both ITS and morphological characteristics can be used to identify the exact Fusarium species causing Fusarium keratomycosis. This allowed us to determine the sensitivity of these species to antifungal drugs that can be used to treat patients with these species of Fusarium.