The datasets are 1) the resistance phenotypes of 6 isogenic lines of rainbow trout challenged to acute hypoxia stress at an early stage (182-187 days post-hatching), 2) the resistance phenotypes of 6 isogenic lines of rainbow trout challenged to acute hyperthermia stress at an early stage (182-187 days post-hatching), 3) the resistance phenotypes of 6 isogenic lines of rainbow trout challenged to acute hypoxia stress at a late stage (455-460 days post-hatching), and 4) the resistance phenotypes of 6 isogenic lines of rainbow trout challenged to acute hyperthermia stress at a late stage (455-460 days post-hatching). The environmental conditions during resistance phenotyping are also given in each of the 4 datasets. Resistance phenotypes were measured as the time before loss of equilibrium. All the information about the rearing and the phenotyping of isogenic lines are provided in the open-access article: "Lagarde, H., Phocas, F., Pouil, S., Goardon, L., Bideau, M., Guyvarc’h, F., Labbé, L., Dechamp, N., Prchal, M., Dupont-Nivet, M., Lallias, D., 2023. Are resistances to acute hyperthermia or hypoxia stress similar and consistent between early and late ages in rainbow trout using isogenic lines? Aquaculture 562, 738800. https://doi.org/10.1016/j.aquaculture.2022.738800"