Melanotic schwannomas are rare tumors associated with the Carney complex that typically arise from spinal nerve roots. They present a diagnostic challenge due to their histological overlap with melanoma. We present the case of a 35-year-old man whose biopsy was diagnosed as melanoma based on histological and immunohistochemical findings. The diagnosis was changed to melanotic schwannoma following examination of his excision specimen and the identification of a PRKAR1A mutation by targeted next-generation sequencing. While PRKAR1A loss is frequently associated with melanotic schwannoma, PRKAR1A mutations are infrequent in melanoma and when present are typically seen in combination with other mutations. We encourage the application of genetic testing to differentiate clinically distinct entities in cases where histological overlap exists. The speed and cost of sequencing technology have advanced to permit its use in cases where the diagnosis is not entirely clear and a change in diagnosis would dramatically alter treatment recommendations.