The present study aimed to address bacterial disease and improve the survival rate of juvenile marbled eels (Anguilla marmorata) with the development of oral bacterial vaccines against Aeromonas hydrophila and Edwardsiella tarda. The vaccines were developed using bacterial cells treated with formalin and encapsulated with 3% sodium alginate or 6% cellulose acetate phthalate (CAP) and formalin-treated bacterial cells which were sonicated for 1.5 hours and encapsulated with 5% of sodium alginate or 9% CAP. The eels’ serum antibody titer significantly increased after oral vaccination, and results from eels intraperitoneally (i.p.) challenged with A. hydrophila and E. tarda, respectively, showed that the highest relative percent survival was obtained at week 8 in the one-time orally vaccinated groups. Eels administered with boosters of the same oral vaccine exhibited a higher antibody titer that was maintained to the 12th week. Due to the higher quantity of antigen in the encapsulated vaccine, the sonicated-antigen vaccine groups demonstrated increased vaccine efficacy compared to the untreated groups. The results show that oral administration with encapsulated vaccine may protect bacterial antigens from stomach acid, thereby enabling antigen-induced immune responses in the eels’ intestine.