We report here a case of a 32-year old female with a history of minor trauma presented with total corneal ulcer and hypopyon in the left eye. Microbiological examination of corneal scraping showed refractile hyphae with asepted branching filaments and black pigmented colonies in multiple solid agar medium. Identification of the organism was made from culture using D1/D2 region of Large Sub Unit (28S rDNA) based molecular technique. Polymerase chain reaction amplified a band with a sequence that was 100% homologous with Lasiodiplodia theobromae. The organism was sensitive to amphotericin B and voriconazole, and demonstrated resistance to itraconazole and fluconazole. Therapeutic keratoplasty was performed followed by recurrence in graft controlled with topical voriconazole and intracameral amphotericin B. Graft failure was reported after three months.