Due to the increase in stocking density, eutrophication of water quality, and high-temperature conditions aggravate the possibility of hypoxia, and inevitably lead to hypoxic stress, affecting the development of its aquaculture industry. We simulated severe hypoxia stress conditions and constructed two different hypoxia tolerance groups. We used next-generation sequencing to analyze the mRNA expression profiles of the brain and liver under hypoxia to clarify the main pathways and metabolic pathways involved in hypoxia, to systematically reveal the reasons for the differences in hypoxia tolerance among different groups. Overall design: We used RNA sequencing to detect the liver and brain mRNA transcriptomes of the golden pomfret the hypoxia intolerance group (Intol) and hypoxia tolerance group (Tol), and compared them (3 vs 3).