Pigmented Bowen's disease is a rare subtype of in situ squamous cell carcinoma of the skin and mucosa, with a potential risk of invasion and metastasis. It is universally accepted that human papillomavirus (HPV) is the cause of genital Bowen's disease. Herein we report an unusual case of pigmented Bowen's disease of the genital area that clinically simulated malignant melanoma. Accurate diagnosis could only be established after histological examination. Polymerase chain reaction (PCR) analysis showed that the lesion harbored HPV 16 DNA. Although pigmented Bowen's disease is rare, it should be considered in the differential diagnosis of all pigmented lesions of the genitalia. This case report highlights the necessity of biopsy and histopathological examination for every suspicious cutaneous lesion.