In aquaculture, acute hyperthermia resistance is a trait of interest in climate change context. However, acute hyperthermia resistance, measured in laboratory conditions as time to loss of equilibrium when exposed to high temperature, is a trait whose underlying physiological mechanisms are not fully understood. It is important to understand these mechanisms to assess the usefulness of acute hyperthermia resistance trait as a predictor of fish ability to adapt to climate change. In the present study, we investigated links between resistance to acute hyperthermia and gene expressions in gills of rainbow trout exposed to heat stress. For this purpose, we phenotyped 6 rainbow trout isogenic lines for acute hyperthermia resistance and 82 genes gills expressions. Expressions were analysed before and after exposition to moderate heat stress (11°C to 23°C in 1H30 then 30 min at 23°C). Genes studied were chosen to represent several physiological functions such as metabolism, immunity, etc. Genes whose expressions were significantly differently expressed between isogenic lines resistant to acute hyperthermia and isogenic lines sensitive to acute hyperthermia were considered as genes potentially involved in acute hyperthermia resistance. Resistant lines differential gene expressions between the beginning and the end of the heat stress were higher for genes associated with O2 transportation and innate immunity and lower for those associated with active ion transportation and gill permeability. This suggests that energy allocation during heat stress is different between resistant and sensitive fish.