In the current research, the prevalence of clones and genes encoding antimicrobial resistance and toxins were examined among 120 strains from nosocomial infections in tehran, Iran.Antimicrobial susceptibility was examined, based on disk diffusion and PCR method to identify resistance and toxin-encoding genes. Based on the polymorphisms in SCC, , and MLST, the isolates were typed.Among 120 isolates, 85 (70.8%) were methicilin resistant MRSA), and 35 (29.2%) were methicilin sensetive MSSA). The tested isolates contained resistance genes, including (90%), (80%), (30%), (26.7%), (10.8%), (11.7%), (40.8%), (14.2%), (45.8%), and (8.3%). The MRSA strains were clustered into six different clones. The most common genotypes included ST239-SCC III/t037 (23.3%), ST239-SCC III/t388 (22.5%), ST22-SCC IV/t790 (8.3%), ST15-SCC IV/t084 (7.5%), ST585-SCC III/t713 (5%), and ST239-SCC III/t924 (4.2%), respectively. ST182/t196 (8.3%) and ST123/t171 (5%) belonged exclusively to MSSA strains. Overall, 10 (66.7%) and 5 (33.3%) out of 15 isolates with genes were attributed to clones ST22-SCC IV/t790 and ST15-SCC IV/t084, respectively. ST22-SCC IV/t790, ST239-SCC III/t037, and ST15-SCC IV/t084, were related to high-level mupirocin-resistant phenotypes.The genetic diversity of was confirmed in our hospitals, and ST239-SCCmec III/t037 showed a relatively high prevalence in our study. It seems that assessment of resistance and virulence genes in different molecular types is necessary for proper antibiotic consumption.