Background and Aim: Methicillin-resistant Staphylococcus aureus (MRSA) causes infectious diseases that are clinically problematic. Methicillin resistance genes are encoded by the mecA gene on the mobile staphylococcal cassette chromosome mec (SCCmec), with SCCmec types I to V being the most prevalent. Staphylococcal protein A gene (spa) typing is a genotyping method designed for S. aureus. This study aimed to use SCCmec and spa genotyping-based methods to identify the genetic diversity of clinical MRSA isolates. Methods: Fifty MDR-MRSA isolates from tertiary hospitals in Egypt were subjected to molecular-based typing using multiplex PCR to identify SCCmec types I to V and detect spa types via spa DNA sequence analysis. Results: The predominant SCCmec types were SCCmec Ⅴ (34%) and SCCmec Ⅳ (32%). The spa sequence analysis revealed 13 definite spa types, with t084 (24.2%) being the most prevalent, followed by t688 (15.1%). Based on both genotyping methods, 20 diverse MRSA clones were identified, with the most predominant MRSA clones being CC15-SCCmecⅤ-t084 and CC15-SCCmecⅣ-t084 (12.1%). Conclusion: MRSA bacteria in Egyptian hospitals are genetically different, indicating that the strains have diverse origins. Thus, regular surveillance of MRSA diversity is required to detect emergent clones for precise epidemiological evaluation and improved procedures to prevent the spread of this superbug.