A 44-year-old woman with known progressive systemic sclerosis was seen at the hospital because of anal discomfort and bloody stool. Digital examination revealed a grayish polypoid lesion in the posterior wall of the anal canal. With a preoperative diagnosis of internal hemorrhoid or anal polyp, the lesion was extirpated. Histopathologically the extripated tumor was malignant melanoma. So rectal amputation with lymph node dissection through abdomino-sacral approach was carried out. About one month later a metastasis to the inguinal lymph node developed. Malignant melanoma has a poor prognosis, because of delayed diagnosis, the high vascularity of the anal region, and high biological malignancy such as vascular and lymphatic spread. Though there was no statistical difference in the prognosis between local resection and rectal amputation, a few patients undergoing rectal amputation could live for more than 5 years. Rectal amputation of the abdomino-sacral method with lymph node dissection is recommended. The disease presents difficulty in diagnosis from macroscopic findings and absolutely demands intraoperative or emergent microscopic frozen section diagnosis.