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Transcriptional regulation constitutes a rapid response of marine organisms facing stressful environmental conditions, such as the concomitant exposure to warming, ocean acidification and hypoxia under climate change. In previous studies, we investigated whole-organism physiological patterns and cellular metabolism in gill and muscle of the marine gastropod Haliotis fulgens in response to increasing temperature (18 degrees C to 32 degrees C at +3 degrees C per day) under hypoxia (50% air saturation), hypercapnia (1000 mu atrn pCO(2)) and both factors combined. Here, we report investigations of the molecular responses of H. fulgens to temperature and identify mechanisms concomitantly affected by hypoxia and hypercapnia. A de novo transcriptome assembly with subsequent quantitative PCR and correlation network analysis of genes involved in the molecular response were used to unravel the correlations between gene expression patterns under the different experimental conditions. The correlation networks identified a shift from the expression of genes involved in energy metabolism (down-regulated) to the up-regulation of Hsp70 during warming under all experimental conditions in gill and muscle, indicating a strong up-regulation of damage prevention and repair systems at sustained cellular energy production. However, a higher capacity for anaerobic succinate production was evicted in gill, matching with observations from our previous studies indicating succinate accumulation in gill but not in muscle. Additionally, warming under hypoxia and hypercapnia kept mRNA levels of citrate synthase in both tissues unchanged following a similar pattern as muscle enzyme capacity from a previous study, suggesting an emphasis on maintaining rather than down-regulating mitochondrial activity.