Previous work has demonstrated local adaptation in populations of redband trout (Oncorhynchus mykiss) occupying desert and montane habitats. To further elucidate the genetic mechanisms of thermal adaptation, gametes were collected from fish at two locations intended to represent warm and cool adapted populations. Gametes were fertilized to produce progeny of a pure warm adapted strain, pure cool adapted strain, and their F1 crosses. When fry reached an average weight of 5 grams, each line was divided into treatment and control groups. Fish in treatment tanks experienced diel temperature cycles over six weeks that reached a maximum of 28.5°C in the afternoon and a minimum of 17.0°C at night, while fish in control tanks were held at a constant temperature of 15°C (spring water). Genome scans of samples from survivors vs. mortalities identified eight candidate genes associated with thermal tolerance. Gene expression results from multiple heat shock genes identified patterns of adaptation across strains, and acclimation to heat stress over time.