Details on the genetics of behavioral and quantitative phenotypes remain limited to a few organisms. Such information is central to understanding both adaptation and speciation, as many of these phenotypes reduce gene flow between taxa [1-3]. Hybrid zones provide an ideal arena for studying this topic, as they consist of recombinant genotypes that allow genetic mapping of traits distinguishing natural populations [4]. We examined the genetic basis of migratory orientation and plumage color, both of which may contribute to speciation, in a hybrid zone between two groups of Swainson's thrushes that differ in these traits. We identified a cluster of SNPs on chromosome 4 strongly associated with migratory orientation. Genes involved with the circadian clock, nervous system, and cell signaling were located here and included candidates implicated in smaller-scale studies of migration in different animal groups, supporting previous suggestions that there is a common gene package for migration [5]. Plumage color was more polygenic than migratory orientation but showed strong associations on the Z chromosome that included SNPs linked to TYRP1, a gene involved in the production of eumelanin. We integrated these results with genomic data from pure populations and found that regions associated with both phenotypes co-localized with regions of elevated relative differentiation between the groups. This finding relates to the literature on islands of differentiation [6-8] by implicating divergent selection in generating these peaks. Together, our results identify specific genomic regions involved in both the regulation of complex phenotypes across animal groups and speciation [9].