The preservation of ion balance and the regulation of body fluid pH despite changes in body temperature are crucial for the maintenance of vital cellular functions in ectothermal animals. We therefore investigated the expression of Na+/K+-ATPase a-subunit (ATN-A1) and the functional consequences in the temperate eelpout Zoarces viviparus acclimated to 13.5 and 3°C in comparison to the confamilial Antarctic Pachycara brachycephalum. In both eelpouts RT-PCR of mRNA isolated from different tissues provided evidence for one Na+/K+-ATPase gene at least, sharing the highest degree of identity to each other (DNA/protein: ~98%) and other fish Na+/K+-ATPase isoform 1 genes (DNA: ~85 %; protein: ~91%). The resulting cDNA clones were used to generate RNA probes for quantitative RNase protection assays. The ATN-A1 gene was expressed in all investigated tissues. Na+/K+-ATPase mRNA expression in liver and gills was increased both in cold acclimated Z. viviparus as well as in cold adapted P. brachycephalum compared to Z. viviparus acclimated to warm temperature. At the functional level maximum activities as well as Arrhenius activation energies were altered during cold acclimation and adaptation in both tissues, arguing for some level of metabolic cold adaptation in the Antarctic P. brachycephalum. However, protein number remained constant during cold acclimation, as determined by two Na+/K+-ATPase antibodies with different isoform specification. Therefore we propose, that transcriptional shifts between different isoforms or post-translational modifications (e.g. membrane composition) or both play an important role in establishing the functional changes during cold acclimation (and cold adaptation), whereas total Na+/K+-ATPase protein number remains constant probably due to space constraints of the membranes.