Primary urethral malignant melanoma is an extremely rare malignancy with early metastasis and often delayed diagnosis, resulted in poor prognosis. Literature on this entity, especially with regard to urinary cytology is limited. We report here an extremely rare case of primary urethral malignant melanoma (MM) developed in a 95-year-old Japanese woman. A urinalysis showed macrophages containing brown granular pigments, and the urinary cytology was positive for atypical cells containing brown pigments suggestive of MM. Pathological examination of the biopsy specimen from the tumor revealed MM of the urethra. Immunohistochemically, the tumor cells showed strong cytoplasmic reactivities against antibodies, HMB-45 and Malan-A. Melanoma cells were immunohistochemically positive for c-Kit in their cytoplasm and cell membrane, although mutations in BRAF V600E and N/K-RAS were not detected. The urinary cytology and immunohistochemistry were useful for the rapid and accurate diagnosis for the urethral MM.