Presented by Joshua I. Brown - Email: firstname.lastname@example.orgLittle is known about the evolutionary history of the Chihuahuan desert endemic Mexican duck (Anas platyrhynchos diazi), which is one of fourteen Mallard-like ducks within the Mallard Complex. Hybridization with mallards (A. platyrhynchos) was originally thought to be a major conservation concern for Mexican ducks, but recent molecular work suggests otherwise. Here, we use a landscape level approach to determine the extent of current hybridization between mallards and Mexican ducks. We collected a total of 266 Mexican ducks across their range, 70 mallards, as well as 62 domestic mallards, including feral Khaki Campbell and game-farm released mallards from three states. We sequenced ~3,500 ddRAD-seq nuclear loci across samples, and report that mallards and Mexican ducks are genetically structured, and that Mexican duck populations follow an isolation-by-distance pattern. Notably, despite previous estimates of wide-spread hybridization, we report that hybridization between Mexican ducks and mallards (wild or domestic) is generally rare (~3%), and lowest of all New World Mallard-like ducks. In fact, we propose that previous estimates of hybridization based on plumage alone were likely inaccurate because traits thought to indicate a hybrid were in fact ancestrally shared between Mexican ducks and mallards. Moreover, several genomic regions under the effects of divergent selection within either Mexican ducks or mallards were recovered, providing support for the possible evolution of isolating mechanisms between the two. Next, we find that Mexican duck populations established in the early 1990s, and now distributed throughout western coastal habitats of Sonora and Sinaloa, were founded by Mexican ducks from Chihuahua. Finally, despite the isolation-by-distance pattern within Mexican ducks that is likely due to high levels of regional fidelity and low or no long-distance dispersal, we report the first genetically vetted Mexican duck collected in California.