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Dissolved oxygen (DO) is crucial for fish farming, and when fish experience hypoxic stress, negative effects such as the disruption of normal physiological activities, a decline in aerobic swimming ability, and feeding restriction will occur. In this study, healthy Epinephelus coioides individuals were subjected to hypoxic (DO = 0.6 ± 0.1 mg/L) and reoxygenation treatments (DO = 6.0 ± 0.1 mg/L), with a normoxic group (DO = 6.0 ± 0.1 mg/L) set as the control. Transcriptome sequencing (RNA-seq) was performed on the brains of E. coioides in hypoxia-sensitive (EBW), hypoxia-tolerant (EBS), and normoxic control (CB) groups. In total, 1174 differentially expressed genes (DEGs) were screened from the three groups. KEGG analysis revealed several pathways, including the HIF-1 signaling pathway, and immune-related pathways such as MAPK signaling, microRNAs (miRNAs), and oxidative phosphorylation pathways enriched in the EBS group, and cAMP signaling pathway enriched in the EBW group. Moreover, a variety of significant hypoxia-responsive DEGs involved in energy metabolism and immune reactions were identified in the EBS and EBW groups. qRTPCR analysis showed that the key DEGs HIF-1α, LDH-A, PPARα, PNP, RAB13, DDIT4, TNF-1, and ALDOA were significantly upregulated in the brain tissues of E. coioides under acute hypoxic stress and that their expression returned to normoxic levels after reoxygenation, indicating that they provided energy to the organism and regulated severe damage and lesions appearing in the brains of E. coioides during hypoxic stress to prolong the survival time of the organism. Altogether, these results suggest that hypoxia disrupts the expression patterns of multiple genes in E. coioides and that these genes may participate in resistance and adaptation to hypoxia in the organisms by regulating apoptosis, proliferation, differentiation, and energy metabolism.