The evolution of disease resistance in plants occurs within a framework of interacting phenotypes, balancing natural selection for life-history traits along a continuum of fast-growing and poorly defended, or slow-growing and well-defended lifestyles. Plant populations connected by gene flow are physiologically limited to evolving along a single axis of the spectrum of the growth-defense trade-off, and strong local selection can purge phenotypic variance from a population or species, making it difficult to detect variation linked to the trade-off. Hybridization between two species that have evolved different growth-defense trade-off optima can reveal trade-offs hidden in either species by introducing phenotypic and genetic variance. Here, I investigated the phenotypic and genetic basis for variation of disease resistance in a set of naturally formed hybrid poplars. The focal species of this dissertation were the balsam poplar (Populus balsamifera), black balsam poplar (P. trichocarpa), narrowleaf cottonwood (P. angustifolia), and eastern cottonwood (P. deltoides). Vegetative cuttings of samples were collected from natural populations and clonally replicated in a common garden. Ecophysiology and stomata traits, and the severity of poplar leaf rust disease (Melampsora medusae) were collected. To overcome the methodological bottleneck of manually phenotyping stomata density for thousands of cuticle micrographs, I developed a publicly available tool to automatically identify and count stomata. To identify stomata, a deep con- volutional neural network was trained on over 4,000 cuticle images of over 700 plant species. The neural network had an accuracy of 94.2% when applied to new cuticle images and phenotyped hundreds of micrographs in a matter of minutes. To understand how disease severity, stomata, and ecophysiology traits changed as a result of hybridization, statistical models were fit that included the expected proportion of the genome from either parental species in a hybrid. These models in- dicated that the ratio of stomata on the upper surface of the leaf to the total number of stomata was strongly linked to disease, was highly heritable, and wass sensitive to hybridization. I further investigated the genomic basis of stomata-linked disease variation by performing an association genetic analysis that explicitly incorporated admixture. Positive selection in genes involved in guard cell regulation, immune sys- tem negative regulation, detoxification, lipid biosynthesis, and cell wall homeostasis were identified. Together, my dissertation incorporated advances in image-based phenotyping with evolutionary theory, directed at understanding how disease frequency changes when hybridization alters the genomes of a population.