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Abstract Understanding interactions between environmental stress and genetic variation is crucial to predict the adaptive capacity of species to climate change. Leaf temperature is both a driver and a responsive indicator of plant physiological response to thermal stress, and methods to monitor it are needed. Foliar temperatures vary across leaf to canopy scales and are influenced by genetic factors, challenging efforts to map and model this critical variable. Thermal imagery collected using unoccupied aerial systems (UAS) offers an innovative way to measure thermal variation in plants across landscapes at leaf‐level resolutions. We used a UAS equipped with a thermal camera to assess temperature variation among genetically distinct populations of big sagebrush (Artemisia tridentata), a keystone plant species that is the focus of intensive restoration efforts throughout much of western North America. We completed flights across a growing season in a sagebrush common garden to map leaf temperature relative to subspecies and cytotype, physiological phenotypes of plants, and summer heat stress. Our objectives were to (1) determine whether leaf‐level stomatal conductance corresponds with changes in crown temperature; (2) quantify genetic (i.e., subspecies and cytotype) contributions to variation in leaf and crown temperatures; and (3) identify how crown structure, solar radiation, and subspecies‐cytotype relate to leaf‐level temperature. When considered across the whole season, stomatal conductance was negatively, non‐linearly correlated with crown‐level temperature derived from UAS. Subspecies identity best explained crown‐level temperature with no difference observed between cytotypes. However, structural phenotypes and microclimate best explained leaf‐level temperature. These results show how fine‐scale thermal mapping can decouple the contribution of genetic, phenotypic, and microclimate factors on leaf temperature dynamics. As climate‐change‐induced heat stress becomes prevalent, thermal UAS represents a promising way to track plant phenotypes that emerge from gene‐by‐environment interactions.