The aquatic animals including fish face many challenges from microorganisms and pathogens while living in aquatic environment. Mucosal surface act as the first line of defence against pathogenic microbes' entry into the internal organs. Therefore, mucosal immune response plays crucial role in combating any external infectious pathogenic intrusion in the fish biological system and limited literature is available on mucosal immunity. In this study, bicistronic vaccine (pGPD+IFN) construct prepared previously was cloned and bulk vaccine plasmids were isolated for vaccination in Labeo rohita against E. tarda. The vaccine was then conjugated with PLGA/Chitosan nanoparticle designated as PLGA/Chi NPs- pGPD+IFN. The vaccine was delivered through the immersion method and experiment were conducted for 70 days. Tissues were collected at 0, 2,4,7,15, & 30 days from mucosal associated tissues (Gill, Gut & Skin/epidermal). Total RNA was isolated from respective tissues and cDNA was synthesized for expression studies of Immunoglobulin gene (IgM, IgD & IgZ) using qRT-PCR. A significant up-regulation of the mRNA expression of IgM, IgD and IgT was observed in gill, gut and skin respectively in immunized fish compared to control fish. The highest expression of IgM was observed in gill followed by gut tissues at 15 day whereas IgD and IgZ highest expression was observed in gut and skin at 30 and 15 day post vaccination (PV) respectively. The remaining fish after sampling were challenge with virulence E. tarda strain at 30 Day PV and morbidity and mortality rate were recorded. The relative percentage survival (RPS) results showed significant (p < 0.05) difference between vaccinated group (60 %) and control group (20%) respectively. This concludes that DNA conjugated PLGA/Chi NPs induce adaptive mucosal immunity and enables effective protective immunity in fish against E. tarda.