A case of clear cell adenocarcinoma and squamous cell carcinoma coexisting in the ovary is presented. These two malignancies were adjacent but were not admixed, and ovarian endometriosis was confirmed concurrently. The clear cell adenocarcinoma was contiguous to monolayered glandular cells with cytological and architectural atypia, while squamous metaplasia with cellular atypia was observed adjacent to the squamous cell carcinoma. We concluded that these two malignancies arose independently from ovarian endometriosis. To our knowledge, this is the first report of such a case.