To make a comparison of PCR assay, Agar Dilution and Disk Diffusion as for detecting Staphylococcal mecA, femA genes.A total of 178 strains of Staphylococci were isolated from three large scale hospitals in Chengdu. Disk Diffusion and staphylococcal mecA, femA gene PCR assay for detecting MRSA were compared with Agar Dilution.The sensitivity and specificity of Disk Diffusion for detecting MRSA were 94.4% and 92.4% respectively. The sensitivity and specificity of Disk Diffusion for detecting MRCNS were 89.5% and 73.7% respectively. Compared with Agar Dilution, Staphylococcus aureus mecA gene PCR assay's sensitivity and specificity were 91.7% and 95.5% respectively. In all the 178 strains of Staphylococci, mecA gene combining with femA gene PCR assay's specificity was up to 97.9%.The detection of femA gene together with mecA gene by PCR is not only an approach for differentiating MRSA from MRCNS, but also a rapid, highly specific method which can be used as an auxiliary method in clinical microbiological laboratory.