Streptococcosis and columnaris diseases caused by Streptococcus iniae and Flavobacterium covae, respectively, crucially impact Asian seabass aquaculture in Thailand. In this study, we built upon research in which Asian seabass larvae were immersed and orally immunized with a bivalent nanovaccine formulated from S. iniae and F. covae. Control and vaccine-primed fingerling fish (2.38 +/- 0.67 g and 5.68 +/- 0.53 cm) from two different nursery farms underwent consecutive vaccination trials and were orally booster vaccinated 2 times. The first and second vaccinations were orally administered on days 0 and 15 at the same concentration (1 x 10(8) CFU/fish) via experimental feed. At 0, 15, and 30 days after the first vaccination (DAFV), tissues from the head kidney, spleen, gills, and intestine were sampled to investigate total IgM, specific IgM to S. iniae and F. covae, innate immune responses, histology, and expression analysis of immune-related genes. The results showed that the nanovaccine strongly increased the total IgM concentration in the head kidney and spleen of vaccinated fish to a significantly greater extent than that in the control group (P < 0.05) for both farms. IgM specific to S. iniae and IgM specific to F. covae, as well as the expression of genes involved in specific immune responses (IgM, IgT, IgD, CD4, MHCII alpha, and TCR alpha) in all target organs, were significantly greater in all vaccinated groups than in the control group (P < 0.05). Histopathological examination revealed greater interbranchial lymphoid tissue (ILT) size, more lymphocyte-like cells in the gills, and increased goblet cell density in the intestines of vaccinated fish than in those of control fish. Furthermore, the fish that received the nanovaccine exhibited a significantly greater cumulative survival rate than those in the control group, regardless of whether the nanovaccine was tested against S. iniae or F. covae. This highlights the effectiveness of the vaccine in stimulating the immune system to provide sufficient disease resistance against both types of diseases in fish.