Black rockfish (Sebastes schlegelii) inhabit the coastal regions of the northwestern Pacific Ocean, including the East China Sea, Yellow Sea, and the coastal areas of Korea and Japan. It is highly favored by consumers because of its delicate flavor and high nutritional content. Black rockfish is among the most economically cultivated marine species in northern China. The juveniles were raised in offshore net cages. The optimum temperature for black rockfish growth ranges from 18 ℃ to 24 ℃. In summer, the seawater temperature sometimes exceeds 28 ℃ in black rockfish farms. As global warming intensifies, long-term exposure to high temperatures in summer will affect the growth and survival of black rockfish cultured in net cages, indicating that the effects of chronic heat stress on black rockfish merit further research. However, the molecular mechanisms underlying the responses of black rockfish to chronic heat stress remain largely unknown. Understanding these mechanisms will improve fish welfare and farm production. Marker genes to monitor heat stress are required to identify heat-resistant fish. In this study, we conducted RNA-seq analysis to characterize the genes and pathways involved in chronic thermal stress responses in the gills, liver, and intestines of black rockfish. Healthy black rockfishes were cultured at a normal temperature (18 ℃) and a high temperature (27 ℃). For the chronic heat stress treatment, water temperature was increased from 18 ℃ to 27 ℃ at a constant rate of 1 ℃ per day, and maintained for 10 days. The gill, liver, and intestinal tissues were used as experimental materials in both the heat stress and normal groups. Total RNA was extracted, and 18 mRNA libraries were constructed and sequenced using the Illumina HiSeq-4000 technology platform. Differentially expressed genes were analyzed using edgeR. Bioinformatic analysis was performed on the GO and KEGG functions of the differentially expressed genes, and the key differentially expressed genes were further validated using RT-qPCR. In total, 306 annotated differentially expressed genes (DEGs) were identified in the gill, of which 96 and 210 were up-and downregulated, respectively. In total, 806 annotated differentially expressed genes (DEGs) were identified in the liver, of which 382 were upregulated and 424 were downregulated. A total of 343 annotated differentially expressed genes (DEGs) were identified in the intestine, among which 162 and 181 were up-and downregulated, respectively. A Venn diagram showed that 12 DEGs were shared among three tissues. And 40, 53, and 49 DEGs were shared between liver and gill, liver and intestine, gill and intestine, respectively. Furthermore, GO functional enrichment analysis revealed that the DEGs were mainly enriched in proteolysis, extracellular region, structural molecule activity, receptor regulator activity, and receptor-ligand activity in the gill; in lipid metabolic process, cellular amino acid metabolic process, cytoplasm, and oxidoreductase activity in the liver; and in oxidation-reduction process, extracellular region, and cofactor binding in the intestine. Among the up-regulated genes under heat stress included the heat shock proteins 90α, period circadian protein homolog 2, serpin H1, and the down-regulated genes included period circadian protein homolog 1. Ten DEGs were subjected to reverse transcription quantitative PCR (RT-qPCR) for relative quantification to assess the differences in gene expression between the normal and high temperature groups. The expression trends observed in the RT-qPCR analysis were consistent with those identified in the RNAseq data, which confirmed the reliability of the transcriptomic sequencing results. These results provide abundant data for further studies on the molecular mechanisms of the chronic heat stress response in Sebastes schlegelii.