Malignant melanoma accounts for less than 3% of all gastrointestinal tract malignancies, and it is mainly metastatic in origin. In contrast, primary melanoma of the small bowel is an extremely rare entity. We report the case of a 34-year-old male who was diagnosed with melanoma involving the ileum most likely secondary in origin. Histologically, the neoplastic cells involved the entire wall thickness, showed nuclear pleomorphism, nuclear pseudoinclusions, abundant eosinophilic cytoplasm, and were immunoreactive for S100, HMB45, and Melan-A. Electron microscopy showed electron-dense complexes that suggested aggregates of melanin. The final diagnosis was given based on the clinical, radiologic and histopathologic correlation. This case demonstrates the need of clinical and histological immunohistochemistry, electron microscopy and molecular studies together to make a correct diagnosis of spindle cell and epithelioid tumors of the gastrointestinal tract.