We report a case of severe pigmented keratitis with poor prognosis, caused by Cladorrhinum bulbillosum. Antifungal treatment with topical natamycin and fluconazole eye drops and oral tablet fluconazole failed to heal the ulcer and resulted in perforation. The causative fungus, C. bulbillosum, was identified on the basis of its typical microscopic features and 98% sequence homology to ex-type isolate CBS 304.90 (accession no. FM955448). The results of an in vitro antifungal susceptibility test indicated that the isolate was susceptible to natamycin, amphotericin B, fluconazole and itraconazole. The present case is the third case of keratitis and the second case of human keratitis. Compromised immunity due to liver cirrhosis could lead to a failed prognosis even when the fungal isolate is highly susceptible to antifungal treatment.