Since 1994, several different inactivated rabies vaccines have been used to immunize domestic animals such as dogs, cats, and cattle in South Korea. The Korean Veterinary Authority has conducted safety and efficacy testes of inactivated vaccines using laboratory animals. In this study, we applied a molecular method to investigate the genetic characterization of the rabies virus (RABV) genes in six commercial inactivated rabies vaccines, and determined the efficiency of two extraction reagents (i.e., sodium citrate or isopropyl myristate) to separate the vaccine antigens from the antigen/adjuvant complexes. Six partial nucleocapsid (N: 181 bp) and five partial glycoprotein (G: 306 bp) genes were successfully amplified with specific primer sets, which demonstrated that sodium citrate is more efficient in than isopropyl myristate in extracting viral RNA from inactivated gel vaccines. In addition, we identified the viral strain of the vaccine by analyzing the nucleotide sequences of the N and the G genes. The nucleotide similarity of the partial N and G genes ranged from 97.1 to 99.4% and from 91.8 to 100% among rabies vaccine strains, respectively, indicating that each manufacturer used different rabies virus strains to produce their vaccines. The molecular method used in this study could also be used to identify viral strains in other inactivated vaccines.