In this study, we investigated the feasibility of using enterovirus HY12 as a vector to express an exogenous hemagglutinin (HA)-epitope tag onto the HY12-encoded VP1 protein via a reverse genetic system. Characteristics of recombinant (r) HY12-VP1-HA marker virus were determined by immunoperoxidase monolayer assay, western blot, electron microscopy, and serum-neutralisation assay. Sequence analysis demonstrated that the marker virus stably maintained the HA-epitope-tag in MDBK cells, with no changes in viral morphological features observed relative to those of the parental rHY12 virus. Furthermore, detection by immunofluorescence assay revealed the expression of HA-epitope tag and VP2 protein, which distinguish the marker virus from parental rHY12 virus. In addition, neonatal mice infected with the recombinant marker virus showed various microscopic pathological lesions and generated anti-HY12 virus and -HA-epitope-tag antibodies. These results indicated that the recombinant marker virus represented a valuable platform to promote the development of novel genetic vaccines.