Integrons are mobilizable platforms-DNA elements with impacts on moving antibiotic resistance genes among bacteria and capable of spreading multi-drug resistance (MDR) in pathogens. Methicillin-resistant Staphylococcus aureus (MRSA) strains are the main cause of community-acquired and nosocomial infections with high mortality and morbidity rates worldwide. This work is mainly aimed at calculating the frequency of Type I, II, and III integrons within multi-drug resistance and Methicillin-resistant S. aureus Isolates in Iran. In this cross-sectional study, 230 clinical isolates of S. aureus were gathered from patients of educational hospitals in the provinces of Iran. These isolates were verified utilizing particular biochemical examinations and then assessed for antibiotic susceptibility through disk diffusion technique and standard procedures were done. Genomic and plasmid DNA of all isolates were extracted using Extraction Kit and PCR assay was used for the detection of Type I, II and III integrons genes. Out of the 230 S. aureus isolates, 136 (59.1%) isolates were MRSA and 141 (61.3%) isolates exhibited the MDR pattern. PCR and sequencing showed that 57 (24.8%) of tested isolates carry Type I integron. Among the isolates investigated, MRSA and MDR isolates showed frequencies of 56.1% and 57.9%, respectively. Type II and III integrons were found in none of 230 isolates. The IntI I gene was present in approximately one-quarter of this study isolates. The great prevalence rate of MDR and MRSA isolates and concurrently the existence of Type I integron among those isolates have been considered an important concern in medical society.