Climate change poses a great threat to cold-water fish species. This is particularly true for lake dwelling cold-water fish as they are limited in their capacity to disperse to avoid stressful conditions. Our ability to predict and plan for the effects of climate change is limited by our understanding of the capacity to adapt to changing conditions found within and among populations. This understanding requires knowledge of the genetic diversity and molecular mechanisms that underpin species’ ability to adapt. Here, we propose a study of the effect differing climates have in shaping molecular responses to thermal stress in several distinct, but geographically close, populations of brook trout (Salvelinus fontinalis). Brook trout of eastern North America is a sentinel cold-water species, with decreasing suitable thermal habitat causing population level extinction. We will use a system of stratified and unstratified lakes as a natural climate change experiment, where the unstratified lake populations persist in thermally stressful conditions, while the stratified lakes provide thermal refuge habitat at the bottom of the lakes. We will take a genomic approach to address two questions: 1) Are there differences in gene expression among lakes and lake types (stratified vs. unstratified) in response to thermal stress, demonstrating local adaptation? and 2) Are there regions of the genome associated with differences in susceptibility and phenotypic response to thermal stress? We will use this information to develop an approach for assessing the genetic diversity associated with thermal adaptation in other brook trout populations. The information gained from this study will be invaluable for understanding the molecular basis for local adaptation and its relation to climate change resiliency planning, and in designing management actions that sustain brook trout into the future.