Geographical distribution patterns of Atlantic cod, Gadus morhua, and Arctic cod, Boreogadus saida, have altered during the last decades to large amounts, driven mainly by warming of water masses. Projections of increasing habitat temperature as well as PCO2 concentrations may lead to stronger adverse effects to their abundance in the future. In general, a species’ fitness at a certain condition could best be monitored through the physiological parameter growth. However, as this fitness parameter is a sum of net free energy, a basic understanding of what process may ultimately limit a species’ performance remains obscure. Within our study we aim to characterize the molecular basis through gene expression patterns that become effective at optimum conditions or critical limits. Farther, we aim to identify gene networks that may contribute to a species robustness or sensitivity. To this end we set up the basis for comparative gene expression analyses by sequencing normalized transcriptomic cDNA libraries for both species. In total, we determined 11,901 orthologous sequences constituting a segment of a shared core-transcriptom. In addition, we found unique sequences that may be responsible for species’ specific varying phenotypic plasticity. Based on all sequences we will build a microarray to analyse transcriptomic patterns under different temperatures and PCO2 concentrations. By combining gene expression data with physiological parameters we want to provide a comprehensive view on molecular mechanisms that shape species’ vulnerability.