One of the most powerful innate immune responses against virus is mediated by the type I interferon (IFN). In teleost fish, it is known that virus infection triggers the expression of ifn and many IFN-stimulated genes but the viral RNA sensors and mediators leading to the IFN production are scarcely known. Thus, we have searched the presence of these genes in gilthead seabream (Sparus aurata) and European sea bass (Dicentrarchus labrax) and evaluated their expression after infection with viral nervous necrosis virus (VNNV) in the brain, the main viral target tissue, and the gonad, used to transmit the virus vertically. In seabream, a resistant fish species to the VNNV strain used, we found an up-regulation of the genes encoding MDA5, TBK1, IRF3, IFN, Mx and PKR proteins in the brain, which were unaltered in the gonad and could favour the dissemination by gonad fluids or gametes. Strikingly, in European sea bass, a very susceptible species, we identified, in addition, transcripts coding for LGP2, MAVS, TRAF3, TANK and IRF7 and found that all the genes analysed were up-regulated in the gonad but only mda5, lgp2, irf3, mx and pkr did in the brain. These findings support the notion that the European sea bass brain innate immune response is unable to clear the virus and points to the importance of the gonad immunity to control the dissemination of VNNV to the progenies, an aspect that is worth to investigate in aquatic animals.