Congenital melanocytic nevi are hamartomatous lesions that develop from the neural crest and arise during odontogenesis. In this report, we present two malignant melanoma cases developed from congenital melanocytic nevi and revealed by gastrointestinal system metastases. The first case was a 71-year-old female who presented with pleural and peritoneal effusion and underwent biopsy due to detection of nodular lesions in the duodenum by endoscopic examination. The second case was a 36-year-old male patient who presented with abdominal pain in whom segmental ileal resection was performed due to mass lesions causing invaginations in the ileum. Histopathological examination of the lesions showed a diffuse neoplastic infiltration comprising the entire mucosal layers. In neoplastic cells having a marked atypia and pleomorphism, immunoreactions with S-100, HMB-45, and Melan A were detected. Both cases were diagnosed as malignant melanoma. Abdominal skin in the first case and the femoral region in the second case exhibited congenital melanocytic nevi, and those lesions were determined to show a transformation towards malignant melanoma in the histopathological studies. Malignant melanoma development in gastrointestinal system may have a primary or metastatic character. Definitive diagnosis always requires detailed clinical, histopathological and immunohistochemical analyses.