Evolutionary adaptation and the connected acclimation capacity of species to changing environmental conditions represent key factors in the composition and dynamics of any ecosystem. In marine environments temperature is one of the major driving forces defining the plasticity of the aquatic fauna. Species adapted to stable environmental conditions seem to be especially vulnerable as a trade-off for being specialized to certain conditions. To characterize molecular trends in thermal adaptation, the cold-stenothermal Antarctic eelpout Pachycara brachycephalum was studied by means of sequence analysis of a normalized cDNA library. DNA/RNA sequences and respective translations were compared to orthologs from a eurythermal congener, the Northsea eelpout Zoarces viviparus. Besides a different repertoire of genes in normalized transcriptomes, position-specific interchanges in the amino acid sequence highly conform with the flexibility hypothesis. According to this hypothesis, a protein may be destabilized in its three-dimensional structure by minimal changes within the amino acid sequence. This destabilization sustains reaction kinetics in the cold. In addition, differences were noted in the encoding of amino acids at DNA level. Within homologous proteins of both zoarcid fish, amino acids of P. brachycephalum are encoded with a preference for AT-richer triplets on the third codon position. This trend promotes less stable transitional states at this level, too, as the base pairing of AT is less stable than that of GC. This may facilitate transcription and translation in the cold and thus constituting an adaptation to the cold habitat conditions of the Antarctic eelpout. The observed trends in fish transcriptomes resolve molecular adaptations that differ significantly on the scale of a whole transcriptome even since the mean annual habitat temperature of both fish differ only by 10°K. Such adaptation may also limit cold-stenothermal organisms in their capacity to successfully acclimate to higher temperatures that are nowadays expected also in the Antarctic realm.