Two different O 2 levels (normoxia: 75–85% O 2 saturation; moderate hypoxia: 42–43% O 2 saturation) and stocking densities (LD: 9.5, and HD: 19 kg/m 3) were assessed on gilthead sea bream ( Sparus aurata) in a 3-week feeding trial. Reduced O 2 availability had a negative impact on feed intake and growth rates, which was exacerbated by HD despite of the improvement in feed efficiency. Blood physiological hallmarks disclosed the enhancement in O 2-carrying capacity in fish maintained under moderate hypoxia. This feature was related to a hypo-metabolic state to cope with a chronic and widespread environmental O 2 reduction, which was accompanied by a differential regulation of circulating cortisol and growth hormone levels. Customized PCR-arrays were used for the simultaneous gene expression profiling of 34–44 selected stress and metabolic markers in liver, white skeletal muscle, heart, and blood cells. The number of differentially expressed genes ranged between 22 and 19 in liver, heart, and white skeletal muscle to 5 in total blood cells. Partial Least-Squares Discriminant Analysis (PLS-DA) explained [R2Y(cum)] and predicted [Q2Y(cum)] up to 95 and 65% of total variance, respectively. The first component (R2Y = 0.2889) gathered fish on the basis of O 2 availability, and liver and cardiac genes on the category of energy sensing and oxidative metabolism ( cs, hif-1α, pgc1α, pgc1β, sirts 1- 2- 4- 5- 6- 7), antioxidant defense and tissue repair ( prdx5, sod2, mortalin, gpx4, gr, grp-170, and prdx3) and oxidative phosphorylation ( nd2, nd5, and coxi) highly contributed to this separation. The second component (R2Y = 0.2927) differentiated normoxic fish at different stocking densities, and the white muscle clearly promoted this separation by a high over-representation of genes related to GH/IGF system ( ghr-i, igfbp6b, igfbp5b, insr, igfbp3, and igf-i). The third component (R2Y = 0.2542) discriminated the effect of stocking density in fish exposed to moderate hypoxia by means of hepatic fatty acid desaturases ( fads2, scd1a, and scd1b) and muscle markers of fatty acid oxidation ( cpt1a). All these findings disclose the different contribution of analyzed tissues (liver ≥ heart > muscle > blood) and specific genes to the hypoxic- and crowding stress-mediated responses. This study will contribute to better explain and understand the different stress resilience of farmed fish across individuals and species.