Although conventional histopathologic examination is still the undisputable mainstay for the diagnosis of melanocytic skin neoplasms, application of molecular testing has experienced tremendous growth and will continue to expand in the future as the need for more specific diagnoses and new targeted therapies evolve. Ancillary molecular methods, including comparative genomic hybridization and fluorescence in situ hybridization, have the potential to provide important new information to challenging cases, and will help improve diagnostic accuracy, particularly in cases in which morphology is not conclusive. Pathologists are increasingly involved in the prospective genotyping of melanoma, which leads to patient stratification in light of the novel personalized therapeutic approaches in the advanced setting.