Mitochondria are essential in adaptation of poikilothermic animals to changing environmental temperature and the related energetic costs. The increase in mitochondrial densities frequently observed in the cold may contribute to higher energetic demands in the cold through mitochondrial maintenance costs and the intrinsic energy dissipation through proton leakage. Mitochondrial uncoupling proteins (UCP) are known to be crucial in thermoregulatory processes in various endothermal animals. To investigate whether uncoupling proteins are involved in thermal adaptation of ectothermal animals, we isolated and characterised the entire genes of UCP-2 for two closely related zoarcid fish species from Antarctic (Pachycara brachycephalum) and boreal (Zoarces viviparus) waters. Identical RNA probes were developed for both species to compare UCP-2 expression levels at different acclimation temperatures as well as between the two fish species.At the RNA level, UCP-2 expression increased considerably with acclimation temperatures above and below habitat temperatures in both species, with constitutively higher UCP-2 transcript concentrations in the eurythermal species Zoarces viviparus. The functional consequences of these changes are discussed.