Freund's complete (FCA) and incomplete adjuvants (FIA), generally applied in subunit shery vaccine, have not been explored on the molecular mechanism of the nonspeci c immune enhancement. As long noncoding RNAs (lncRNAs) play vital regulating roles in various biological activities, in this study, we examined the genome-wide expression of transcripts in the liver of European eel (Anguilla anguilla, Aa) inoculated with FCA and FIA (FCIA) to elucidate the regulators of lncRNAs in the process of Edwardsiella anguillarum (Ea) infection and Aa anti-Ea infection using strand speci c RNA-seq. After eels were challenged by Ea at 28 d post the rst inoculation (dpi), compared to the control uninfected eels (Li group), the control infected eels (Con_Li group) showed severe bleeding, hepatocyte atrophy and thrombi formed in the hepatic vessels of the liver, although eels inoculated with FCIA (FCIA_Li group) also formed slight thrombi in the hepatic vessels. Compared to the FCIA_Li group, there was about 10 times colony forming unit (cfu) in the Con_Li group per 100 µg liver tissue, and the relative percent survival (RPS) of eels was 50% in FCIA_Li vs Con_Li. Using highthroughput transcriptomics, differential expressed genes (DEGs) and transcripts were identi ed and the results were veri ed using uorescence real-time polymerase chain reaction (qRT-PCR). Interactions between the differential expressed lncRNAs (DE-lncRNAs) and the target DEGs were explored using Cytoscape according to their co-expression and co-location relationship. We found 13499 lncRNAs (10176 annotated and 3423 novel lncRNAs) between 3 comparisons of Con_Li vs Li, FCIA_Li vs Li and FCIA_Li vs Con_Li, of which 111, 110 and 129 DE-lncRNAs were asertained. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of DEGs targeted by DE-lncRNAs revealed these DEGs mainly involved in single-organism cellular process in BP, membrane in CC and binding in MF, and KEGG pathways showed that the target DEGs in co-expression and co-location enriched in cell adhesion molecules. Finally, 118 DE-lncRNAs target 1161 DEGs were involved in an interaction network of 8474 co-expression and 333 colocation related links, of which 16 DE-lncRNAs play vital roles in anti-Ea infection. Taken together, the interaction networks revealed that DE-lncRNAs underlies the process of Ea infection and Aa anti-Ea infection.