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Dissolved oxygen (DO) is essential for most aquatic species. Hypoxia can cause abnormal behaviors and arrested development of the golden pompano (Trachinotus blochii). Thus, it is necessary to increase the DO level to relieve hypoxic stress. However, few studies have focused on the impact of different reoxygenation rates on cultured fish. This study investigated the effects of two reoxygenation treatments on T. blochii after 12-h-hypoxia (1.9 ± 0.2 mg/L): gradual reoxygenation (GRG, increased DO level within 3 h) and rapid reoxygenation (RRG, increased DO level within 10 mins). The result of microRNA (miRNA) sequencing showed that miR-122 was the most abundant miRNA in the liver, which was similar to other teleosts, confirming that miRNAs are highly conserved. Our results revealed that in the RRG treatment, the downregulated expression of miR-34a-5p increased the expression of Casp9 , improving cell survival. The downregulated expression of miR-2188-3p increased the expression of MDM2 , regulating apoptosis. The high expression of miR-144-5p downregulated NF-κB , regulating immune responses. In contrast, in the GRG treatment, miR-34a-5p promoted the expression of ALDOA to accelerate the anaerobic metabolism. The low expression of miR-2188-3p enhanced aerobic metabolism by increasing the expression of VEGFA. The miR-34a-5p, miR-144-5p, and miR-2188-3p in the liver adjusted hypoxic stress by regulating apoptosis and cell survival and increasing the anaerobic metabolism. Our results indicate that different reoxygenation rates correspond to different miRNA adaptation strategies. Additionally, this study provides a new perspective for further studying the effect of miRNA on the reoxygenation rate and the resulting influence on the golden pompano after hypoxic stress. The figure includes experimental design and basic results, the red in black dotted box indicates the up-regulated, while the blue indicates the down-regulated. [Display omitted] • Hypoxia downregulated miR-144-5p results in the upregulation of NF-κB and VEGF. • Rapid reoxygenation inhibits miR-34a-5p and promotes Casp9 to ensure cell survival. • MiR-34a-5p and miR-2188-3p participate in metabolic regulation during gradual reoxygenation. [ABSTRACT FROM AUTHOR]