Abstract: Objective To understand the distributions and drug resistance of methicillin-resistant Staphylococcus aureus (MRSA) strains isolated from animal food samples, animal clinical samples and human clinical samples, and provide theoretical support for the control of MRSA infection and clinical treatment. Methods Animal food samples, animal clinical samples and human clinical samples were collected from different areas of Anhui province for MRSA isolation and culture. The identification and drug susceptibility testing were done using Vitek auto-microbiological analysis system. The mecA was detected with PCR, and pulsed-field gel electrophoresis (PFGE) and homology analysis of MRSA with software BioNumerics were conducted. Results A total of 690 samples of 3 kinds of samples, including 450 animal food samples, 90 animal clinical samples and 150 human clinical samples, were collected from Huaibei, Hefei and Maanshan of Anhui and 82 MRSA strains were isolated, including 14 strains from animal food samples (3.1%), 23 strains from animal clinical samples (30.0%) and 45 strains from human clinical samples (25.6%). The drug susceptibility test indicated that all the 82 isolates were sensitive to vancomycin, linezolid and dalfopristin, but resistant to penicillin and oxacillin, and all the isolates had different resistances to cefazolin, erythrocin, clindamycin, tetracycline, gentamicin, levofloxacin, rifampicin, sulfamethoxydiazine and ampicillin, the differences among the isolates with different sources were not significant. PFGE results showed that the 82 isolates had 49 PFGE patterns, indicating that they shared low homologies. Conclusion The isolation rates of MRSA in animal clinical samples and human clinical samples were higher than that in animal food samples. The differences in drug susceptibility among the isolates with different sources had no significance. PFGE and homology analysis showed that all the isolates had weak genetic relationship, indicating polyclonal characteristics of the isolates.