Adenocarcinoma in association with chronic anal fistula is a rare disease which gives rise to difficult problems of diagnosis and treatment. A case of mucinous adenocarcinoma arising on a long standing fistula in ano is described. A patient with a long history of mucinous discharge, pain and perianal induration underwent a biopsy of the external opening of the fistula that showed mucinous infiltrating adenocarcinoma. After a colonoscopy and a preoperative abdominal CT scan, she underwent a successful abdominoperineal resection with adjuvant chemoradiation therapy. Diagnosis of this condition is often difficult; deep and multiple biopsies of the fistulous tracks or perianal mass are necessary to establish the diagnosis. An accurate staging of the neoplasm, using endorectal ultrasound, NMR or CT scans is needed to plan the appropriate treatment. Recent studies have shown that locally advanced anal adenocarcinomas could benefit from pre or postoperative chemoradiation therapy. However, an accurate and complete removal of the tumor, which usually entails abdominoperineal resection, is often necessary to achieve radicality. Despite new therapy protocols, the prognosis of mucinous adenocarcinoma is still poor, mostly due to its advanced nature at the time of diagnosis. This reinforces the importance of biopsy of all perianal abscesses and fistulas for early detection and treatment.