Abstract: 【Objective】To investigate the molecular regulation mechanisms in gill tissue of Exopalaemon carinicauda under gradually changing hypoxia-reoxygenation stress,so as to provide theoretical reference for the breeding of hypoxia tolerance strains(species)of E. carinicauda.【Method】By simulating the formation process of hypoxia in the natural environment,gill tissues were collected at 0(control),3 and 6 h,and 1 and 8 h after reoxygenation,respectively. Transcriptome sequencing analysis was performed using Illumina HiSeq^TM 4000 sequencing platform. Unigenes were obtained by filtration and Trinity assembly. Nr,Swiss-Prot,KEGG and COG/KOG databases were selected for annotation analysis. The differentially expressed genes(DEGs)were screened and their trends were analyzed on the Omicsmart platform. Then GO functional annotation analysis and KEGG signal pathway enrichment analysis were performed,and five DEGs were randomly selected for real-time quantitative PCR(qRT-PCR)validation.【Result】A total of 93227 uni genes whose range were from 201 to 35402 bp were obtained through transcriptome sequencing,with their average length of 834 bp and the N50 of 1352 bp. 4750 genes were identified as DEGs through pairwise comparison between groups,of which the up-regulated genes were 3557 and the down-regulated genes were 2829. More than fifty percent were significantly enriched in six gene expression trends(P<0.01):Profile 0 was enriched in 415 genes;Profile 5 was enriched in 201 genes; Profile 11 was enriched in 371 genes;Profile 13 was enriched in 841 genes;Profile 17 was enriched in 387 genes and Profile 18 was enriched in 411 genes.The DEGs in six trends were annotated to metabolic processes,cellular processes,single organism process,cell,cell parts,macromolecular complex and catalytic activity by GO functional analysis. The KEGG signaling pathway enrichment analysis showed that DEGs in Profile 13 were enriched in 86 pathways at most and significantly enriched in ribosome,carbon metabolism,oxidative phosphorylation,biosynthesis of amino acids,protein processing in endoplasmic reticulum,glycolysis or gluconeogenesis,glutathione metabolism and protein export.【Conclusion】The gill tissues of E.carinicauda synthesizes protein and increases metabolic capacity to resist hypoxia in the early stage of hypoxia stress. But with the prolongation of hypoxia,both substance synthesis and energy metabolism were affected and decreased. After reoxygenation,with the prolongation ofreoxygenation,the protein synthesis and energy metabolism gradually recover to level under normal oxygen.