A genetic link between cutaneous melanoma and thyroid cancer (TC) has been identified. A high percentage of both melanomas and papillary carcinomas of the thyroid harbors a recurrent mutation (i.e., BRAFV600E) in the BRAF oncogene. Herein, we report the case of a 65-year-old man with papillary TC and cutaneous malignant melanoma metastatic to masseter muscle, both characterized by BRAF mutation. This is one of the rare reports in which a complete molecular characterization has been performed. As the patients with papillary thyroid carcinoma have a higher risk of malignant melanoma and vice versa, continuous monitoring of such patients, with either of these tumors is necessary. Fineneedle aspiration cytology is useful as shown in the present case.