Adaptation to prevailing thermal conditions is crucial to the survival of any organism. Temperature dictates the stability and conformation of biomolecules, and populations must ensure that the structure of their enzymes is properly tuned to environmental temperatures. Populations that exist across habitats which differ chiefly by temperature are expected to show patterns of local adaptation, whereby the highest level of genetic differentiation is found at loci involved in thermal adaptation. However, detecting genetic loci associated with thermal response in wild populations is often hampered by the confounding effects of phenotypic plasticity. We collected hatchling larvae of a montane leaf beetle, Chrysomela aeneicollis, from equal-elevation sites in three isolated drainages along a north-south latitudinal gradient California’s Sierra Nevada, and raised them to third instar in the laboratory under common garden conditions. Larval running speed was measured before and after a 36˚C heat treatment, and whole genome data was obtained from 206 larvae using Illumina paired end sequencing. We performed an FST outlier test to identify single-nucleotide polymorphisms with the highest level of differentiation between the three populations, as well as an association analysis to identify SNPs associated with running speed following heat treatment. We found that native drainage did not significantly affect larval running speed, which indicates that the common garden design successfully controlled for phenotypic plasticity. This experiment provides insights into how genomic variation allows organisms living at the edge of their thermal tolerance to adapt to changing conditions.