Abstract: In order to compare the immunogenicity of Duck circovirus（DuCV） Ⅰ and Ⅱ Cap protain, the Cap gene of DuCV-BJ strain（HM162350.1, DuCVⅠ） and DuCV-FJ strain（EF370476.1, DuCV Ⅱ） were selected as reference sequences for antigen epitope prediction, codon optimization and synthesis, and cloned into pET-28 a vector which then was transformed into BL21（DE3） host bacteria for induced expression, and the recombinant proteins were obtained. Balb/c mice were immunized with the purified recombinant protein, and the level of specific antibody IgG and cytokines interferon-γ（IFN-γ）, interleukin（IL）-2, and IL-4.The results showed that the average antigen index of Cap protein of DuCV-BJ strain and DuCV-FJ strain were 1.727 and 0.505, respectively. After codon optimization, the codon adaptation index（CIA） increased from 0.89 to 1.00. The recombinant plasmids pET28 a-BJ and pET28 a-FJ were successfully expressed in E. coli;Balb/c mice immunized with recombinant proteins rCap-BJ and rCap-FJ, both of which could induce mice to produce specific antibody IgG. After three immunization, IgG levels in rCap-FJ and rCap-BJ groups were very significantly higher than those in the control group（P＜0.01）, but there was no significant difference between rCap-FJ group and rCap-BJ group（P＞0.05）; the levels of IFN-γ, IL-2 and IL-4 in rCap-FJ and rCap-BJ groups were very significantly higher than those in the control group（P＜0.01）. The results suggested that the recombinant proteins rCap-BJ and rCap-FJ could stimulate Balb/c mice to produce specific immune response, and had good immunogenicity.