Rectal melanoma is extremely rare. Its histologic variability and difference in immunohistochemical (IHC) expression may hinder the correct diagnosis. Seventy-three years old Korean woman complained of bloody stool and found a 2cm sized rectal pedunculated polyp on colonoscopy. There was some disparity in IHC expressions as well as cytological morphology between biopsy and surgically resected specimen. When strong immunoreactivity of S-100 is encountered in anorectal lesion with unusual morphology, multiple IHC analysis and high suspicion of anorectal melanoma could lead to correct diagnosis.