Strangles is a highly prevalent, extremely contagious, and occasionally lethal infectious disease affecting horses worldwide. Prophylactic antibiotics are ineffective in prevention of disease but are recommended for exposed horses at the first sign of fever and any horse obviously ill from strangles or with complications and there is an urgent need of a cost-effective, safe, efficacious vaccine. In the present study, we sought to develop effective vaccines by fusing the Streptococcus equi subspecies equi (S. equi) antigen SeM with the flagellin of Salmonella abortus equi FljB. We also explored the immunogenicity and efficacy of this candidate vaccine in mice and horses by intramuscular injection. Mice and horses immunized with FljB-SeM DNA vaccine showed high levels of specific antibody and increased production of IFN-γ and IL-4. This confirmed that both Th1 and Th2 type responses were induced. The mice survival rate was significantly higher after immunization with FljB-SeM than with SeM alone. The FljB-SeM DNA could strengthen both the Th1 and Th2 immune responses compared to SeM and could provide better protection against S. equi. This technique could help develop a candidate vaccine for S. equi infection.