Epithelioid cell tumors presenting in the gastrointestinal tract are uncommon, but when they arise, arriving at a correct diagnosis is important. We report a case of anal malignant melanoma in an 82-year-old man who microscopically showed an epithelioid malignant tumor simulating a gastrointestinal stromal tumor. C-kit stain and Melan-A were diffusely and strongly positive, while HMB-45 was focally positive. This case illustrates the potential pitfall of relying on a single antibody or inadequate panel of immunohistochemical stains to confirm the diagnosis. We recommend to apply an adequate immunohistochemical panel which includes S-100 protein, HMB-45 and Melan-A in order to make an accurate diagnosis, and discuss the differential diagnosis and surgical treatment modalities.