Bovine brucellosis is a zoonotic disease distributed worldwide and characterized by abortion and reduced fertility in cows. Since brucellosis eradication programme in Iran uses vaccination, test, slaughter and quarantine as control measures, it is essential to distinguish vaccine strains from strains that cause infections among vaccinated cattle herds. We developed and evaluated a multiplex polymerase chain reaction (PCR) assay to identify and differentiate the vaccine strains from wild field isolates, including all Brucella types usually found in cattle in Iran. Two pair primers were used to amplify eri and wbo regions of DNA sequences those strain-specific targets for B. abortus S19 and RB51 vaccine strains. This multiplex PCR method evaluated with DNA from reference strains, two vaccine strains and 29 field strains of Brucella. The results showed that the multiplex PCR can differentiate Brucella isolates into three categories: strain 19 (S19), strain RB51 and field strains. This PCR assay was successfully used, compared with traditional method to differentiate of S19 and RB51 from field Brucella isolates.