Malignant melanoma (MM) can mimic soft tissue (ST) and epithelial neoplasms. An immunoperoxidase (IP) panel and a morphologic comparison of the primary are used in diagnosis, which can be difficult when the morphologic and IP profiles of a metastatic lesion simulate those of an ST neoplasm. Through the comparison of known genetic abnormalities in primary and metastatic neoplasms, a definitive diagnosis can be suggested on the basis of the finding of identical allelic losses through the use of microdissection (MD) and the polymerase chain reaction (PCR). Genetic alterations involving the p16 gene on chromosome 9p21 have been observed in MM. We present the case of a 56-year-old man with known MM in whom multiple metastatic lesions to the skin and an adrenal gland developed during a 5-year period. A fine-needle aspiration (FNA) of a new ST buttock lesion was performed; the specimen had cytologic features different from those of the primary neoplasm and simulated a possible primary ST neoplasm. We attempted to make a definitive diagnosis of MM in the FNA of the ST buttock lesion through a genetic comparison with the primary neoplasm as well as with the other metastatic sites. Direct-visualization MD was performed on histologic glass slides of the primary and adjacent tissue (normal control), and the metastatic lesions, along with malignant cell clusters from the buttock lesion FNA. DNA was extracted and PCR amplified with primers D9S171 and IFNA for the p16 locus at the 9p21-22 region. Loss of heterozygosity for the D9S171 marker at the p16 gene locus was identified in all of the neoplastic tissue tested. Normal skin elements did not show deletion. The combination of MD and PCR are powerful tools that can be used for the comparison of genetic abnormalities in primary and metastatic neoplasms with unusual morphologic features to help support a diagnosis with a noncontributory IP.