Species from different branches of the tree of life often look and function in similar ways. These similarities provide compelling evidence of parallel evolution of phenotypes as a result of shared ecological pressures or developmental constraints. Studies in a broad range of organisms have shown how morphological, physiological, and behavioral traits contribute to fitness. However, the molecular mechanisms behind adaptation and parallel evolution are poorly known. Do shared phenotypes in different species involve the same underlying nucleotides, genes, or functional gene classes? To address this question, we propose a comparative genomic study of Podarcis, a phenotypically diverse group of lizards distributed throughout the Mediterranean. Multiple Podarcis species have independently evolved a suite of traits that includes a green dorsum, blue lateral spots, robust body and head, and high aggression. Remarkably, these traits share a developmental origin in the embryo’s neural crest cells, suggesting that genetic associations between traits may have favored the repeated evolution of a phenotypic syndrome. To test this hypothesis, we will employ broad genomic sequencing of species that express the syndrome in certain geographic locations but not in others. We will then perform genomic scans of population differentiation to identify the genes and genetic variants associated with the syndrome in each species. We will compare the degree of molecular and phenotypic parallelism across species by incorporating a large phenomics dataset composed of quantitative trait measurements. Finally, to uncover how adaptive genetic variants originate, spread, and persist, we will integrate genetic signatures of adaptation with inferences of population structure and history. This combined approach will provide unprecedented insight into the factors behind repeated evolutionary outcomes – a pervasive feature of life on Earth.