Numerous studies have demonstrated that the C. irritans can be efficiently propagated in the animal model golden pompano (Trachinotus blochii), especially in the process of intensive high-density culture, which causes large-scale infection and triggers bacterial invasion is a devastating blow to the golden pompano industry. This is in sharp contrast to the low sensitivity of S. oramin to C. irritans. Overall design: we simulated an experiment of artificially infecting C. irritans on S. oramin and T. blochii. RNA-seq was utilized to detect the transcripts in the gill of S. oramin and T. blochii at different times of infection, used the bioinformatics analysis of the pathways and compared the variations of all the involved differentially expressed genes (DEGs). Please note that the identifiers in processed data (e.g. Sig_T000001, Trachinotus_GLEAN_10000138, etc.) are self-numbered in the transcriptome sequencing, and then these identifiers were annotated based on the genome (as included in two annotation files (Tra_gene.nr.xls and Sig_gene.nr.txt)).