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Understanding patterns and mechanisms underlying local adaptation is becoming increasingly important for species conservation amid anthropogenically driven environmental change. Alpine systems are experiencing particularly intense pressure from environmental change resulting from increased rates of warming and corresponding loss of snow and ice. We integrate morphological and genetic analyses to identify traits important for local adaptation in one of the highest elevation breeding birds in North America, the Sierra Nevada Gray-crowned Rosy Finch. We performed an in-depth analysis of how traits with known links to thermoregulation in birds such as wing length, bill size, and feather microstructure vary between two populations at sites with contrasting climate and environmental conditions. We identified loci underlying these traits using a genome-wide association study and further examined regions of the genome related to altitude adaptation and cold tolerance using F ST outlier tests. Together, these results indicate that temperature, food availability, and alpine landscape features may impose multifaceted and potentially conflicting selective pressures on morphological traits important to adaptation in alpine birds. Overall, this work represents one of the first in-depth analyses of the genetic basis of adaptation in an alpine specialist songbird.