Although many clinicopathological studies of malignant melanoma of the conjunctiva have been reported, there have been no studies of the expression and gene mutations of KIT and PDGFRA in melanoma of the conjunctiva. A 69-year-old Japanese woman consulted our hospital because of black mass (0.7 × 0.7 × 0.6 cm) in the conjunctiva. A biopsy was taken. The biopsy showed malignant epithelioid cells with melanin deposition. Immunohistochemically, the tumor was positive for S100 protein, HMB45, p53, Ki-67 (labeling=30%), KIT and PDGFRA. The tumor was negative for pancytokeratins (AE1/3 and CAM5.2). A genetic analysis using PCR-direct sequencing revealed no mutations of KIT gene (exons 9, 11, 13, and 17) and PDGFRA gene (exons 12 and 18). The pathological diagnosis was conjunctival melanoma. Despite chemotherapy, the patient developed multiple metastases of melanoma, and died of melanoma 7 years after the biopsy. In conclusion, the author reported a case of melanoma of conjunctive expressing KIT and PDGFRA proteins without gene mutations of KIT and PDGFRA.