Adjustments in mitochondrial properties and capacities are crucial in acclimatization to seasonal cold as well as in evolutionary cold adaptation of marine ectotherms. While long-term compensatory increments in the aerobic capacity of fish tissues have frequently been described in response to cold, much less is known about the transitional phases and the gene expression patterns involved. We therefore investigated the time course of adjustment to acute cold in liver of the eurythermal eelpout Zoarces viviparus. Whereas citrate synthase activity rose progressively in liver, cytochrome c oxidase activity was not altered during cold acclimation. Species-specific RNA probes were used to determine the mRNA levels of the respective genes. Citrate synthase mRNA (nuclear encoded) displayed a delayed, transient increase in response to cold, such that transcript levels did not parallel the change in enzyme activity. Comparison with enzyme activities and mRNA levels of the confamilial Antarctic Pachycara brachycephalum indicate cold compensated citrate synthase activities in liver of the cold adapted species. The ratio of citrate synthase and cytochrome c oxidase activities was elevated in both, acclimation and adaptation to cold, indicating enhanced citrate synthesis over respiratory chain capacities in cold-adapted liver mitochondria. Such a shift may support enhanced lipid synthesis typically found in the cold. The ratio of enzyme activity and transcript levels differed largely between Z. viviparus populations from the Baltic Sea and the North Sea, indicating the influence of unidentified parameters other than temperature. Altogether, transcript levels may not necessarily be tightly correlated with enzyme activities during thermal adaptation and thereafter. The time course of the acclimation process indicates that regulation at the translational and post-translational level predominates in the adjustment to moderate thermal challenges.