In order to obtain the gene P12X3C of foot-and-mouth disease virus (FMDV O/China99) that includes full length P1, 2A, 3C and part of 2B and 3B, the site mutation strategy was used. The recombinant plasmid pcDNA3.1/P12X3C was transfected into BHK-21 cells. The capsid proteins of FMDV expressed in BHK-21 cells were confirmed by sandwich-ELISA and indirect immunofluorescence test. Then the plasmid pcDNA3.1/P12X3C was administered to guinea pigs intramuscularly, and purified FMDV O/China993D protein expressed in yeast cells was injected together with pcDNA3.1/P12X3C. Anti-FMDV antibodies were detected by indirect ELISA, the T-lymphocyte proliferation response was tested by MTT assay, and neutralizating antibodies titers were analyzed by micro-neutralization assay. The result showed that the plasmid pcDNA3.1/P12X3C was able to express immunocompetent proteins of FMDV in BHK-21 cells. Furthermore, anti-FMDV antibodies were elicited and increased by plasmid pcDNA3.1/P12X3C in the second week after vaccination. Neutralizating antibodies were induced and the T-lymphocyte proliferation response was enhanced after vaccination. In the challenge test, all of guinea pigs vaccinated with pcDNA3.1/P12X3C were fully protected from FMDV challenge. However, the result obtained from animals that were injected with protein 3D together with plasmid pcDNA3.1/P12X3C was not satisfied. In conclusion, the results encouraged further work towards the development of a DNA vaccine against FMDV and provided the basis of research for DNA vaccine.