The chitosan nanoparticles (CNPs) conjugated bicistronic DNA vaccine (pGPD+IFN) containing GAPDH gene of Edwardsiella tarda and IFN-γ gene of Labeo rohita was found to induce high protective immunity in L. rohita against virulent E. tarda challenge in our previous study. However, for conducting vaccination trials in aquaculture farms, it is essential to circumspect various biosafety issues concerning the use of DNA vaccines in food fishes as per international guidelines. In this context, the present study was undertaken to evaluate the persistence, bio-distribution and environmental transmission of the DNA vaccine (pGPD+IFN) to provide the basis for commercial application. The experimental study involves complexation of the DNA construct with chitosan coated PLGA (poly lactide-co-glycolide) nanoparticles (Chi/PLGA NPs) in order to enhance the vaccine uptake by the host through immersion route. The mean particle size (267.4 nm) and zeta potential (+27.mV) of the Chi/PLGA- pGPD+IFN vaccines assists in giving higher stability to the pDNA as well as facilitate in easy uptake and wide tissue distribution. The bio-distribution and persistence results showed that the DNA vaccine was localised at the immunization administration surfaces of the host (gill, gut and skin+muscle and not in kidney and liver) and remained persistent for 14–30 days post immersion treatment. The low copy numbers (<4 copies/100 ng of host DNA) of the pDNA in the tissue samples cancel out the possibility of pDNA integration into host genome. In addition, the negative results concerning the environmental transmission of the DNA vaccine substantiate the safety of the constructed vaccine.