Because foot-and-mouth disease virus (FMDV) remains a great problem to many livestock of agricultural importance, safe, effective vaccines are in great need. DNA vaccine would be a promising candidate but the design remains to be optimized. VP1 gene of FMDV strain O/ES/2001 was linked to three copies of either porcine or murine C3d or four copies of a 28-aa fragment of murine C3d containing the CR2 receptor binding domain (M28). The resultant plasmids encoding C3d/M28-VP1 fusion or only VP1 as control were immunized guinea pigs. Both cellular and humoral immune responses were evaluated and protection was observed after virus challenge. As a result, although the plasmid encoding only VP1 could elicit virus-binding antibody detected by ELISA, splenocyte proliferation, IL-4 and IFN-gamma production, the levels were significantly less than C3d/M28-VP1 fusion. Furthermore, VP1 failed to induce neutralization antibody and protect animals against virus challenge, while murine C3d-VP1 fusion efficiently induced neutralization antibody response and provided 87.50% of the animals with complete protection and 12.50% with partial protection. Among murine C3d, M28, and porcine C3d, the adjuvant effect of murine C3d is strongest, followed by porcine C3d, and last murine M28. In conclusion, the fact that C3d genes, when coupled to VP1 gene, are able to greatly enhance the protective immune response of VP1 DNA in guinea pigs suggests that C3d-VP1 DNA chimera has a significant potential for use as a novel DNA vaccine against FMDV.