Mitochondrial uncoupling protein 1 (UCP1) is known to be crucial in thermoregulatory processes in various endothermic animals, and its homologues are widely distributed among vertebrates, invertebrates and plants. Mitochondria are essential in the adaptation of poikilothermic animals to changing environmental temperature. The increase in mitochondrial densities frequently observed in cold adapted ectotherms may contribute to higher energetic demands through mitochondrial maintenance costs and the intrinsic energy dissipation through proton leakage.To investigate whether uncoupling proteins are also involved in the thermal adaptation of ectothermic animals, we isolated and characterised the entire genes of UCP2 for two closely related zoarcid fish species from Antarctic (Pachycara brachycephalum) and boreal (Zoarces viviparus) waters. We developed identical RNA probes for both species to compare UCP2 mRNA expression levels at different acclimation temperatures and between muscle and liver tissues. In addition, Western Blot analysis was performed to examine thermal regulation of UCP2 expression at the functional, ie. protein level.Zoarcid UCP2 is a highly conserved 313 amino acid protein, belonging to the mitochondrial membrane carrier family. At both RNA and protein levels, UCP2 expression increased considerably with acclimation temperatures above and below habitat temperatures in the two species, with the mRNA expression patterns being reflected on the protein level. Although the Antarctic eelpout P. brachycephalum, which occurs from the Antarctic Peninsula up into high Antarctic waters, is considered to be more stenothermic than its boreal eurythermic relative Z. viviparus, it appears to have kept the ability to regulate the expression of one of the central proteins involved in the energy metabolism at similar ratios.The functional implications of these findings for the thermal adaptation of zoarcids will be discussed in the context of global warming scenarios.