Global warming is expected to increase the frequency and intensity of heatwaves, resulting in more common combined acute hyperthermia and hypoxia conditions in fish farms. Such poor thermal and oxygenation conditions induce problems, including growth losses, increased pathogens pressure and mortality. Selective breeding is a promising solution to improve resistance to non-optimal water quality. Indeed, genetic variability to survive in acute hyperthermia or hypoxia conditions has been proved in fish. However, the characterization of these traits is not yet detailed enough to include them in a selection program. Here, we investigated the ranking stability of genotypes for acute hyperthermia or hypoxia resistances over age and between acute hyperthermia and acute hypoxia resistances. To this end, we established rankings of six isogenic lines of rainbow trout (Oncorhynchus mykiss) for their resistance to acute hyperthermia and hypoxia stress factors at 6 and 15 months. The experimental design was robust with more than a hundred fish per line and age. There were statistically significant resistance variations among lines confirming the potential of genetic selection for these traits. Hyperthermia and hypoxia resistance rankings were found stable 1 year apart for most genotypes. Therefore, it would be possible to select for resistance to hyperthermia and hypoxia at an early stage. No overall relationship was found between acute hyperthermia and hypoxia resistance traits: some lines were resistant to both stress factors while others were resistant to one but sensitive to the other. This indicates no strong antagonistic genetic effects between acute hyperthermia and hypoxia resistance traits in rainbow trout.