Foot-and-mouth disease is a highly contagious viral disease of cloven-hoofed animals. The availability of a vaccine for differentiating infected from vaccinated animals (DIVA) is crucial for the control and eradication of Foot-and-mouth disease virus (FMDV). Because traditional inactivated vaccines may contain trace nonstructural proteins interfering with the DIVA, we hypothesized that mutant FMDV with deletion of immunodominant epitopes may be valuable. Our previous study has generated a full-length cDNA clone (pBSAs) of FMDV serotype Asia 1 isolated in China. In this study, a B-cell epitope was identified in the 3A region of a nonstructural protein (NSP) by anti-FMDV cattle sera. Furthermore, we generated recombinant FMDV (rvAs-3A14D) by selectively deleting 14 amino acids (position 91-104) in the 3A region of the NSP. Following in vitro transcription and transfection in BHK-21 cells, we successfully rescued the rvAs-3A14D from BHK-21 cells. Characterization of the rvAs-3A14D revealed that the infectivity, antigenicity, and replication kinetics in BHK-21 cells and virulence in mice of the rvAs-3A14D were similar to that of its parent virus. Notably, the mutant rvAs-3A14D only replicated well in BHK-21 but did poorly in primary calf kidney cells. These data suggest that the recombinant FMDV with deletion of this epitope in the NSP may be potentially used as a candidate inactivated vaccine. Therefore, the application of the marker vaccine and differential diagnostic tests may open a promising new avenue for the development of a vaccine for DIVA.