The European eel (Anguilla anguilla), has experienced a dangerous decline in recruitment, yield and stock over the last 30 years and this decline is likely to continue into the future. Several major threats are responsible for this situation, including overfishing of glass eels for consumption, new infections by introduced pathogens, dams and blocking of migration routes. The lack of knowledge concerning the biology of this species represents a handicap to the conservation and recovery of the population. Nevertheless,the eel farming industry is increasing, therefore it could be considered one of the major risks for wild eel stock perpetuation, which is threatened principally by the lack of knowledge of the complete reproductive cycle of the European eel and by emerging bacterial, viral and parasite diseases. Vibrio vulnificus is the aetiological agent of warm-water vibriosis, a disease that constitutes the main threat to eels under culture conditions, provoking important outbreaks and can be an opportunistic pathogen for humans. V. vulnificus uses a novel characterized virulence and survival system namedMARTX (multifunctional repeat in toxin) that it is supposed to trigger a cytokine storm when it is produced in blood during the infection. It is also involved in the colonization of the gills, to invade internal organs and causes death by septicemia. We sequenced an eel immune-enriched transcriptome with Roche 454, and the data has been used to create new molecular tools for further research. We have also designed a custom eel-specific microarray (4x44K, Agilent). Our research has been focused on eel-vibrio interaction, how the host responds to the challenge and the importance of MARTX system of the bacteria for the colonization. Different challenges were performed using wild type strain (CECT4999) and Rtx double mutant strain (CT285) to evaluate mucosal immunity in the gills, the principal portal of entry.We also studied the early immune response of circulating leukocytes and the role of the erythrocytes, as one of the target cells of the lytic activity of this bacterium. Results obtained by RT-qPCR and ISH on gills demonstrate the immunocompetent function of this tissue, based on the expression and localization of immune-relates genes such as, TLRs, cytokines, chemokines and signalling molecules. Microarray studies describe key genes expressed after vibrio infection analyzed across 12h post-challenge on gills and blood (leukocytes and erythrocytes separately), specific host response against vibrio Rtx toxin, as well as, a possible function of erythrocytes in the immune response.