As a consequence of global climate change, acidification and warming of the worlds’ oceans and their possibly adverse impacts on marine organisms have come into the focus of scientific research. However, while many physiological and ecological impacts have already been identified, influences on the molecular mechanisms shaping the physiological phenotype and especially the limits of compensatory capacities of an organism are still unclear. Here, we combined comprehensive analyses of gene and protein expression to identify regulatory mechanisms and relevant processes in the great spider crab Hyas araneus. As a first step, a transcriptome was assembled de novo to enable differential expression analysis and protein identification. Based on the sequence data obtained from different next-generation sequencing techniques (454; Illumina), a total of 20,479 transcript sequences could be generated. As a second step the newly reached steady state in gene expression was determined in gill tissue collected from specimens exposed under different experimental conditions for 10 weeks. The differential gene expression profiling revealed a shift in steady state from control (390 µatm) to intermediate (1,120 µatm) and high (1,960 µatm) levels of PCO2. At 5 °C genes related to acid-base regulation, energy metabolism and the stress response were upregulated at intermediate PCO2, whereas high PCO2 induced a relative reduction in expressionto levels closer to controls. Similar patterns were found at elevated temperature (10 °C). Both conditions revealed a strong coordination of processes involved in acid-base and metabolic regulation, and in the stress response. Expression profiles at intermediate PCO2 indicate enhanced capacity inacid-base regulation through upregulation of a V-ATPase, at the expense of enhanced energy demand, met by an upregulation of the electron transport system (ETS). Elevated metabolic costs may lead to increased oxidative stress as reflected in upregulated antioxidant defence enzymes. The concomitant upregulation of transcripts related to cell structure indicates that the cytoskeletonmay be a main target of oxidative stress. These changes were attenuated at even higher PCO2, possibly as a result of limited compensation in acid-base status and metabolic down-regulation. Our findings indicate a PCO2 dependent threshold beyond which compensation by acclimation displays progressive failure. Since regulatory adjustments are not limited to the transcriptome the study was complemented by a subsequent analysis of protein expression. To identify intra-specific variations in gene regulation under variable environmental conditions, such analyses were carried out in two populations from a latitudinal gradient (Spitsbergen: N 78°58.635'; E 11°29.454' – Sweden: N 58°15.336’; E 11°26.891’). In general, protein abundance patterns corresponded to the transcriptomic response. The abundance pattern of proteins directly and indirectly related to oxidative stress also indicated that hypercapnia causes oxidative stress. Furthermore, the observed accumulation of cell structure related proteins at intermediate PCO2 supports the hypothesis that the cytoskeleton is a main target of oxidative stress. A strong response of cuticle proteins to intermediate PCO2 at 10°C was only observed in the Swedish population indicating a potential variation in ocean acidification effects between populations. The Swedish population displayed a high capacity of acid-base compensation at elevated temperature (16 °C) and high PCO2. As an uncompensated extracellular acidosis can elicit metabolic depression, the capacity for acid-base regulation being enhanced through gene expression may result in delayed metabolic depression. At the same time, this might result in energy demand increasing further. The present thesis indicates limited ability of the stenoecious crustacean H. araneus to compensate for the effects of ocean acidification with and without concomitant warming. Limited compensatory capacities may result in reduced fitness of this and other species of osmoconforming crustaceans and may lead to far reaching consequences for their biogeographic distribution and their competitiveness at ecosystem level.