Melanoma is the leading cause of death among cutaneous neoplasms. Best outcome relies on early detection and accurate pathologic diagnosis. For the great majority of melanocytic tumors, histopathologic examination can reliably distinguish nevi from melanomas. However, there is a subset of melanocytic tumors that cannot be definitively classified as benign or malignant using histopathological criteria alone. These tumors are usually diagnosed using terms that imply various degrees of uncertainty in regards to their malignant potential and create the possibility for over or undertreatment. For such tumors, additional ancillary tests would be beneficial in adjudicating a more definitive diagnosis. In recent years, DNA-based molecular ancillary tests, specifically comparative genomic hybridization and fluorescence in situ hybridization, have been developed to help guide the diagnosis of ambiguous melanocytic proliferations. This study will present an updated overview of these two major ancillary tests, which are currently being used in clinical practice to assist in the diagnosis of challenging melanocytic neoplasms.