Abstract: The goal of this study was to prepare the alginate-chitosan microcapsules containing the Srr-protein of Streptococcus iniae, and to determine its immune effect in channel catfish by oral route. The alginate-chitosan-Srr-protein microcapsules were prepared by an emulsification method, and the encapsulation efficiency, drug-loaded rate, and immunogenicity integrity were tested. Healthy fish were divided into 4 groups, named Srr group, Srr-microcapsules group, empty-microcapsules group, and control group to immune, respectively. The serum antibody level was detected by an indirect ELISA method, and serum non-specific indexes were detected by reagent kits. 4 weeks after the immunization, the relative percent survivals (RPSs) of each group were calculated by challenging the fish with S. iniae, and the mRNA levels of immune related genes were analyzed by real-time PCR. The alginate-chitosan-Srr-protein microcapsules showed round or oval in shapes, with a mean diameter of 4.26±1.13 μm, an encapsulation efficiency of 92.38%, and a drug-loaded rate of 19.41%. Western-blot indicated a good immunogenicity of the microcapsules. The peak of antibody titer appeared at the 4th week after the immunization, among which, antibody titer in the Srr-microcapsules group was the highest. The serum total protein, T-SOD and lysozyme activity of Srr-microcapsules group were obviously higher than those of the other groups. The relative percentage of survival in Srr-microcapsules group was 60%. The results of real-time PCR presented that mRNA levels of immune related genes in kidneys and spleens from the Srr group increased more notably than those in the other groups during the 24h to 48h post injection. In conclusion, the alginate-chitosan-Srr-protein microcapsules vaccine was able to protect channel catfish from S. iniae infection.