This study aimed to characterize the methicillin-resistant S. aureus strains circulating on the skin of individuals with acne. S. aureus isolates were screened for methicillin resistance by methods including, oxacillin agar (OA), cefoxitin disk diffusion (CDD), and PCR for the mecA gene. The mecA-positive methicillin-resistant S. aureus (MRSA) strains were examined for the presence of the Panton-Valentine leukocidin (PVL) gene and typing based on the Staphylococcal cassette chromosome mec (SCCmec). Thirty-seven S. aureus strains were isolated from 78 skin swab samples. Eighteen isolates were identified as positive for the mecA gene. The OA and CDD methods showed lower sensitivity than PCR in MRSA screening. Sixteen MRSA isolates were recorded as multidrug-resistant. Isolates showed a high proportion of phenotype resistance to clindamycin, gentamycin, erythromycin, and linezolid. Eight strains of MRSA carried the PVL fusion gene. In the molecular epidemiology of MRSA, the most predominant were SCCmec types II and III. The rest was SCCmec type IV. Consequently, the spread of multidrug-resistant MRSA with genetic diversity could raise public health concerns. This study indicated the urgency of determining antibiotic resistance and epidemiological characteristics of MRSA in treating and controlling the spread of this pathogen.