Lizards in the genus Anolis have radiated extensively within and among islands in the Caribbean. Here, I provide a prospectus for identifying genes underlying adaptive phenotypic traits in anoles. First I review patterns of diversification in Anolis and the important morphological axes along which divergence occurs. Then I discuss two features of anole diversification, the repeated, convergent evolution of ecomorphs, and phenotypic divergence among populations within species, that provide opportunities to identify genes underlying adaptive phenotypic variation. While small clutch size and difficulty with captive rearing currently limit the utility of quantitative trait locus analyses, comparative analyses of gene expression, and population genomic approaches are promising.