Ecological genetics has entered the genomic era, with one of its main goals to identify genes underlying ecologically important traits. In this talk I will discuss several ways to connect genotype to phenotype in non-model systems. I illustrate these approaches using natural populations of mice (Peromyscus polionotus) that have recently colonized the sandy dunes of Florida's Gulf and Atlantic coasts. In this novel environment, these “beach mice” have evolved many new traits relative to their mainland counterparts, most strikingly a unique pigmentation pattern driven by natural selection for crypsis. I first discuss how we identified the genes responsible for this rapid color adaptation and then describe how this approach can be extended to other phenotypic traits (from morphology to behavior) and to other species. Finally, I will examine the question of what having “the genes” in hand can really tell us about adaptation to novel environments, specifically, and the ecological and evolutionary process, more generally.