Equine herpesvirus 1 (EHV-1) induces serious respiratory infections, viral abortion, neurological signs, and neonatal mortality in horses. Despite the use of vaccines, EHV-1 infection also causes a high annual economic burden to the equine industry. The poor immunogenicity of and protection conferred by EHV-1 vaccines are the major factors responsible for the spread of EHV-1 infection. The present study examined the immunogenicity of a novel DNA vaccine co-expressing FliC, a flagellin protein, in Salmonella abortus equi and the gD protein of EHV-1. Mice and horses were immunized intramuscularly with the vaccine, and mice were challenged with EHV-1. Immunofluorescence and western blotting revealed that FliC and gD can be efficiently expressed in cells. This novel vaccine significantly increased gD-specific antibody and interferon gamma (IFN-γ) levels in immunized mice and horses. Compared with controls, the viral load and morbidity were markedly reduced in FliC-gD-immunized mice after they were challenged with EHV-1. Furthermore, the immunogenicity of FliC-gD in a natural host was tested. Our results indicate that vaccinated mice and horses exhibit increased humoral and improved cellular immune responses.