To better understandthe immune response mechanism of fish gill-associated lymphoid tissue to pathogens, the transcriptome sequencing was performed for the gill tissue from healthy and Vibrio anguillarum infected flounder (Paralichthys olivaceus) in this study with the differentially expressed genes (DEGs) analyzed with GO, KEGG, GSEA and other bioinformatics methods. In total, 620 DEGs were obtained, which included 334 up-regulated genes and 286 down-regulated genes. Eight DEGs were randomly selected for validation of the accuracy and reliability of RNA-seq data by real-time qPCR. The results showed that the expression trend of these eight genes was consistent with the transcriptome sequencing results. The enrichment analysis indicated that the DEGs were enriched in the terms related to autophagy and immune response activation and regulation. The immune-related pathways such as complement and coagulation cascades, leukocyte transendothelial migration, NOD-like receptor signaling pathway, JAK-STAT signaling pathway were activated, and the pathways related to disease and cell adhesion were also significantly enriched. It was found that the lectin genes related to complement activation and antibacterial immunity were up-regulated. The C-type lectin represented by CD209 and MBL changed significantly and was the hub gene in the gene interaction network. As the hub genes of the interaction network, pattern recognition receptors tlr13 and nlrc3 were also significantly up-regulated, and played a key regulatory role in antibacterial mucosal immunity. In addition, the expressions of apoptosis related genes (boka and bcl2l15), phagocytosis related genes (lyg and pla2g4c), mucin gene muc5ac, muc5b and muc19, mucosal defense barrier related genes (cldn3d and esama), and T and B lymphocyte related genes also changed significantly, which were involved in the mucosal immune responses. These results provided a theoretical basis for better understanding the mucosal immune response mechanism of teleost to pathogen invasion.