Methicillin-resistant Staphylococcus aureus (MRSA) is an emerging cause of morbidity and mortality worldwide. This work aimed to study the occurrence of multidrug-resistant MRSA (MDR-MRSA) in tertiary Egyptian hospitals and determine the antimicrobial susceptibilities and the genetic relatedness of isolates for epidemiological assessment. A total of 170 S. aureus isolates were collected from two Egyptian tertiary hospitals in Cairo, between September 2017 and December 2018. MRSA isolates were identified using the conventional microbiological methods and confirmed by the PCR assays targeting nuc gene, a surrogate marker of S. aureus and the mecA gene for genotypic identification of methicillin resistance. Antimicrobial susceptibility was determined using the Kirby-Bauer disk diffusion method and the isolates were grouped into different antibiotypes based on their antibiograms. The genetic relatedness among MDR-MRSA isolates was determined by ERIC-PCR-based molecular typing. High prevalence of MRSA isolates was identified (138/170, 81.2%) with 79% of isolates (109/138, 79%) being MDR-MRSA. MRSA isolates were resistant to diverse classes of antimicrobials including β-lactams, aminoglycosides and macrolides. Among MRSA isolates, the highest resistance rate was to each cefoxitin and penicillin (100%) and the highest susceptibility was to linezolid (92%). Based on the antibiograms of 109 MDR-MRSA isolates, 52 antibiotypes were determined, and 46 different ERIC fingerprints were identified among MDR-MRSA antibiotypes. MRSA infections remain a noteworthy problem in Egyptian hospitals. MDR-MRSA isolates showed significant genetic diversity indicating the alarmingly high prevalence. Studies should be performed frequently, even in each healthcare setting, to determine the epidemiology of MRSA isolates and their antimicrobial susceptibility profiles for effective control measures of MRSA infections and better healthcare management.