Background: The current study was designed to compare the genes expression levels of MHC-П, IL-8 and IgM in the head kidney and liver (central organs), as well as gill tissue (mucosal surface) of juvenile rainbow trout. Materials and Methods: Juvenile rainbow trout were immunized with gamma-irradiated and formalin inactive trophonts with/without alginate nanoparticles against Ichthyophthirius multifiliis. On day 20 after bath-immunization, fish in all the treatments, except negative control, were exposed to live trophonts. On the 30^th day, fish tissues were analyzed by real-time PCR. Results: The IL-8 expression up-regulated in the kidney, hepatic and gill of immunized fish with irradiated and formalin inactive trophonts plus alginate nanoparticles and non-immunized fish challenged with live trophonts (P<0.05). The MHC-II showed up-regulation in gill and kidney of immunized fish and non-immunized fish challenged with live trophonts while hepatic MHC-П was up-regulated in immunized fish with formalin inactive trophonts plus alginate nanoparticles (P<0.05). A significant increase in the IgM expression was detected in gills of immunized fish with irradiated trophonts with/without alginate nanoparticles and formalin inactive trophonts plus alginate nanoparticles (P<0.05). The renal IgM showed up-regulation in all of treatments (P<0.05). A significant increase in the hepatic IgM expression was in immunized fish via irradiated trophonts with/without alginate nanoparticles (P<0.05). Conclusion: These findings indicated that the higher expression of IgM, MHC-II and IL-8 at the gill, kidney and liver could prove the potential of the entire treatments to enhance both mucosal and systemic immune responses in immunized fish with gamma irradiated trophonts against I. multifiliis.