Abstract Hypoxia can influence fish growth, survival and on larger scales, population structure. These effects may be influenced by water temperature, and may vary intra-specifically with genotype. In Atlantic cod ( Gadus morhua L.), the two haemoglobin homozygotes ( Hb-I⁎11 and Hb-I⁎22) vary in oxygen affinity at different temperatures, which is thought to correspond to variation in hypoxia tolerance. We therefore tested if hypoxic avoidance behaviour in cod 1) depends on ambient temperature and 2) is modified by haemoglobin genotype. In a laminar flow choice box, we subjected juvenile cod to an initial phase of non-escapable hypoxia, and a subsequent recovery phase, where one habitat was kept at 20% O 2 saturation while the other was raised in steps to full saturation. The experiment was performed at 5 and 15 °C with Hb-I⁎11 and Hb-I⁎22 cod. Cod responded to inescapable hypoxia by reducing their overall swimming speed and then, at the initial levels of the recovery phase, avoiding the most hypoxic habitat, irrespective of temperature or genotype. Fish recovered quickly as O 2 levels increased, as evidenced by increased swimming speed and time spent in the most hypoxic habitat. The avoidance response depended strongly on temperature: the relative reduction in speed and avoidance of the most hypoxic habitat was more pronounced at 15 than at 5 °C. During the recovery phase, stressed fish initially maintained a higher swimming speed in the most hypoxic habitat. However, as O 2 increased, swimming speed in both habitats converged. This point of convergence occurred at a lower O 2 saturation at 5 °C. Fish ventilation rate in inescapable hypoxia was also higher at 15 °C. Haemoglobin genotype did not influence either ventilation rates or the nature of the hypoxic avoidance response at either temperature, but Hb-I⁎11 cod swam faster than Hb-I⁎22 cod in normoxia at 15 °C. Our results indicate that increased temperature limits the ability of cod of both haemoglobin genotypes to exploit hypoxic habitats. This may have negative future consequences for coastal cod stocks in light of increasing global temperatures and eutrophication in coastal waters.