In the western U.S., the Pacific salmonids (Oncorhynchus spp.) are of significant cultural, socioeconomic and ecological importance. However, despite decades of conservation efforts, their continued decline remains a great concern. Two critical factors impacting the sustainability of salmon and steelhead populations in the Pacific Northwest include genetic introgression of captive-reared hatchery fish and climate warming. Although salmonid hatcheries have been recognized as having a valuable role in restoring wild stocks, gene flow from domesticated hatchery fish into wild populations presents obstacles for conservation. Additionally, climate change is predicted to continue to increase stream temperatures in the Pacific Northwest, which is particularly hazardous for cold-water dependent Oncorhynchus spp., as their physiology, behavior, and distribution are crucially linked to temperature. Here these factors were investigated using clonal lines of rainbow trout (Oncorhynchus mykiss) by evaluating phenotypic responses to these two factors in the context of developing management protocols to facilitate their sustained existence.