Staphylococcus aureus is a common pathogen causing hospital infections. The increasing rate of healthcare-associated infections caused by methicillin-resistant Staphylococcus aureus (MRSA) in developing countries has led to many public health problems. This study aimed to investigate the molecular epidemiology as well as the antibiotic resistance pattern of clinical isolates of MRSA from Southern Iran. A total of 135 S. aureus isolates were collected from the patients referred to three hospitals in South Iran. The phenotypic and genotypic diagnosis of MRSA isolates was performed by disk diffusion and PCR methods, respectively. The antibiotic resistance pattern for MRSA isolates was performed using Kirby-Bauer method. The molecular epidemiology of isolates was performed by MLST, Spa typing and SCCmec typing. From 135 S. aureus isolates, 50 (37%) MRSA strains were detected from which two different sequence types including ST239 and ST605 were identified. SCCmec type III was the most common profile (50%) and t030 was the predominant spa type (48%) among the strains. The MRSA isolates had the highest resistance to penicillin (100%), tetracycline (88%), levofloxacin (86%), ciprofloxacin (84%), erythromycin (82%), gentamicin (80%), and clindamycin (78%). The results of this study show that the most common genetic type among the MRSA isolates was ST239-SCCmec III/t030. The rapid and timely detection of MRSA and the administration of appropriate antibiotics according to the published antibiotic resistance patterns are essential. Furthermore, the continuous and nationwide MRSA surveillance studies are necessary to investigate clonal distribution and spreading of MRSA from community to hospitals.  Kulcsszavak: MRSA, mecA gene, SCCmec typing, Spa typing, MLST