The potential for rapid adaptive evolution is a subject of great interest in evolutionary biology. I took a population genomics approach to study the contemporary evolution of northeastern coyotes (Canis latrans) via hybridization and ecological specialization. I genotyped 96 single nucleotide polymorphisms (SNPs) in a broad geographic sample of 427 northeastern coyotes. First, I examined the prevalence, spatial distribution, and ecology of admixture. I found that northeastern coyotes form an extensive hybrid swarm with individuals being highly admixed with wolves (C. lupus) and dogs (C. familiaris). Coyotes in areas of high deer density are genetically more wolf-like, suggesting that natural selection for wolf-like traits may result in local adaptation at a fine geographic scale. Second, I investigated whether ecological factors can influence genetic structure in coyotes inhabiting the complex, fine-grained mosaic of different habitats characteristic of the Northeast. I found a cryptic genetic pattern consistent with the hypothesis of metapopulation structure conforming to a mosaic of forested, agricultural, and urban habitat types. High deer densities also explained a small but significant proportion of genetic variation. Given the recency of the coyote range expansion into the Northeast, these findings demonstrate the rapid formation of ecological barriers to gene flow in a few generations. Lastly, I examined the molecular basis of local adaptation by analyzing five SNPs associated with ecologically important morphological traits. I provided the first documented evidence of any wild canids with homozygous mutant genotypes in these five SNPs. Coyotes with mutant genotypes are morphological outliers or peripheral individuals, indicating a clear association of morphological and genetic variation. A substantial reduction of gene flow across habitats is apparently mediated by the density of white-tailed deer, a main prey species; and strong diversifying selection is acting on the genetic architecture that underlies morphological traits related to predation. These results suggest that a localized area of high deer density is mediating morphological adaptation and ecological specialization in coyotes. This dissertation represents the most extensive genomic investigation of eastern coyotes, integrating landscape genetics, evolutionary ecology, and the emerging field of functional wildlife genomics.