With increasing environmental temperatures causing concern for the status of freshwater fishes, captive breeding programs may become increasingly important for conservation efforts as well as to support fisheries. Although captive broodstocks provide reliable gamete sources for production stocking, prolonged generations under hatchery conditions selection for hatchery conditions (domestication) and reduced phenotypic plasticity to novel environmental stressors. We assessed the effects of rearing temperature and number of generations spent in captivity on the survival and quality (indicated by lack of malformations) of long-term (F20+) and newly-captive (F1) strains of Ontario hatchery brook trout (Salvelinus fontinalis) with shared genetic history. We found that elevated temperatures decreased likelihood of survival between the hatched and fry stages. Additionally, we found that elevated temperature reduced fry quality of F1 fish whereas F20+ fish were less thermally sensitive, suggesting no reduction in plasticity due to captivity. The combined effects of elevated rearing temperatures and number of hatchery generations suggest that selection for captivity can occur rapidly (in one generation) even under benign conditions, and that additive stressor effects of captivity and temperature may impact newly established strains.