Abstract: The present study aims to investigate the antimicrobial resistance,the distribution of efflux pump genes, and the relationship between the distribution of efflux pump genes and the antimicrobial resistance of bovine methicillin-resistant Staphylococcus aureus (MRSA). The antimicrobial resistance and frequency of efflux pump genes of MRSA were detected by the disk diffusion method and PCR, respectively. The results showed that all 79 MRSA isolates were resistant to penicillin, gentamicin and kanamycin, followed by ciprofloxacin (94.9%), levofloxacin (94.9%), clindamycin (87.3%) and tetracycline (79.7%). Moreover, all isolates were sensitive to nitrofurantoin, quinatudine/dafopretin, neostigmine/trimethoprim and linezolid. PCR results showed that all MRSA isolates carried the efflux pump genes norA, norB, norC, sepA, mepA and mdeA, follwed by qacA/B (24.1%). smr was not found in these isolates. Statistical analysis showed that there were significant correlations between the frequency of norA, norB, norC, sepA, mepA, mdeA and qacA/B and resistance phenotype of penicillin, gentamicin, kanamycin, ciprofloxacin, levofloxacin, clindamycin, rifampin and tetracycline (P<0.01), respectively. These results revealed high antimicrobial resistance to common antibiotics, which indicating that antimicrobial susceptibility testing should be performed prior to clinical administration for selecting suitable antimicrobial agents. Finally, the potential threat of high prevalence of efflux pump genes in MRSA should be of concern.