Ecological genetics is increasingly recognized as critical to understanding interactions among organisms and ecosystem processes. Using a common garden with pure and hybrid cottonwood trees of known genotype, two years of field surveys, and a cafeteria feeding experiment, we link introgression of Fremont genetic markers, condensed tannins (a genetically based plant trait), and foraging by beavers. These data support two major arguments. First, hybridization is an important mechanism for the transmission of ecologically functional traits. Second, links between a genetically based plant trait in a dominant riparian-forest tree species and the foraging behavior of beavers, an ecosystem engineer, emphasize that genetically based plant traits can directly and indirectly link population, community, and ecosystem processes.