A 56-year-old female patient was admitted, complaining of hematochezia. She was preoperatively diagnosed with poorly-differentiated carcinoma of anorectum with metastases in the lung and mesorectal lymph nodes, and underwent abdominoperineal resection of the rectum. The immunohistochemistry of the rectal tumor showed positive for vimentin and c-kit, and negative for AE1/AE3, S-100, a-SMA, LCA and CD34, which was compatible with gastrointestinal stromal tumor (GIST). Regardless of the administration of imatinib mesylate, multiple metastases in the brain, bone, adrenal glands and inguinal lymph node proceeded in a short term. An excisional biopsy of the inguinal lymph node was performed and immunohistochemistry of the specimen showed positive for S-100, melan-A, HMB45 and tyrosinase. Therefore, we concluded that amelanotic anorectal melanoma (AMM) metastasized to the lymph node, and rechecked the immuno histochemistry of the anorectal tumor. The anorectal tumor showed positive for melan-A, HMB45 and tyrosinase, but negative for S-100. As far as we know, there are few reports of AMM with S-100 negative and c-kit positive. In such cases, making a differential diagnosis between AMM and GIST of the anorectal region can be very confusing.