Abstract: OBJECTIVE In the present study, we modified multilocus variable number tandem-repeats fingerprinting (MLVF) and evaluated the classification ability of modified MLVF, in order to establish a methicillin-resistant Staphylococcus aureus (MRSA) genotyping method with easy operation, high discrimination power and low cost. METHODS The capacity of modified MLVF was evaluated against 42 MRSA reference strains, and we compared the modified MLVF with pulsed field gel electrophoresis (PFGE) and variable number tandem repeat sequence analysis (MLVA) on 116 strains collected from six hospitals in northeast China. RESULTS The discriminatory ability of the modified MLVF was 100% against the 42 reference strains. Modified MLVF, PFGE and MLVA divided the 116 clinical strains into 28 types (Simpson's diversity index SID=0.855), 28 types (SID=0.854) and 27 types (SID=0.816), respectively. Modified MLVF had better performance than MLVA in distinguishing between the most popular clone ST239 and other clones. The consistency between modified MLVF and PFGE at clone cluster level (adjusted Rand's index, AR =0.989) was superior to MLVA (AR index =0.765). CONCLUSION The improved MLVF has the advantages of high discrimination power, high consistency with the golden standard PFGE typing, simple operation, high throughput and low cost. It is suitable for the conventional hospital laboratories to conduct molecular typing of MRSA and provides a powerful tool for regular infection control and molecular epidemiological study.