In this study, juvenile turbot Scophthalmus maximus were vaccinated with attenuated Edwardsiella tarda (EIBAV1) and reared at two different densities, low density (LD), (5.25 ± 0.02) kg m -2, as control group and high density (HD), (20.53 ± 0.05) kg m -2, as experimental group. Only density was considered as the variable. Five weeks after vaccination, the transcriptomes of spleen and head kidney from the turbot in two groups were analyzed with RNA-Seq technology. A total of 447 million reads were assembled into 41136 genes with an average length of 1274 bp and a N 50 size of 2295 bp. A comparison of gene expression between HD and LD groups revealed 1155 differentially expressed genes (DEGs). Enrichment and pathway analysis of the 10 immune-related DEGs showed the centrality of toll-like receptor signaling pathway, cytosolic DNA-sensing pathway and platelet activation in the host immune responses. The 5 overexpressed inflammatory cytokines and 5 downregulated signal-regulated cytokines genes are covered by these immune-related DEGs. It was inferred that cells suffer damage and the immune response is restrained in turbot under crowding stress.