Uncoupling proteins (UCP), capable of increasing proton leakage across the inner mitochondrial membrane, may play a role in the temperature dependent setting of energy turnover in animals (and their mitochondria). Therefore, the genes and expression of fish UCP were investigated in the Antarctic eelpout Pachycara brachycephalum and a temperate confamilial species, the common eelpout Zoarces viviparus. UCP full-length cDNA was amplified from liver and muscle using RT-PCR and rapid amplification of cDNA ends (RACE). The fish UCP mRNA consists of 1906bp in P. brachycephalum and of 1876bp in Z. viviparus. Both zoarcid sequences contain open reading frames of 939bp, encoding 313 amino acids, with 98 and 99% identity, respectively. Protein sequences of zoarcid UCP are closest related to fish and mammalian UCP2. For analysis of temperature dependent expression common eelpouts were cold-acclimated from 10°C to 2°C and Antarctic eelpouts were warm-acclimated from 0°C to 5°C. Identical cDNA probes for both species were developed to investigate fish UCP mRNA expression, and protein expression levels were detected by Western Blot in the enriched membrane fraction. During cold-acclimation in Z. viviparus, mRNA levels increased by a factor up to 2.0, protein levels increased up to 1.5, in line with mitochondrial proliferation during cold-acclimation. Despite decreased mitochondrial protein content, in Antarctic eelpout UCP levels rose upon warm acclimation by a factor up to 2.0 (mRNA) and 1.6 (protein), respectively. Besides the ongoing discussion of UCP function in vertebrates, the data are indicative of a significant role of fish UCP in thermal adaptation of fish mitochondria.