Background: Staphylococcus aureus is a major bacterial pathogen that causes nosocomial and community- associated infections with high rates of morbidity and mortality. In recent years, an increase in the incidence of infections caused by methicillin resistant S. aureus (MRSA) has been observed; with increased antibiotic resistance not only to B-lactam antibiotics, but also to other classes, thus, leaving few therapeutic options. To effectively control infections with MRSA and to plan strategies for empirical treatment, it is important to undertake studies delineating the prevalence and clonality of MRSA isolates in a particular region. Aims and objectives: The major objectives of this study were to: (i) estimate the prevalence of MRSA at Sultan Qaboos University Hospital (SQUH) and (ü) to gain understanding of the epidemiology of the MRSA clones as revealed by use of molecular typing. Material and methods: A total of 269, consecutive, non-repeat isolates recovered from clinical specimens between March and December, 2011 at SQUH were collected. Screening for methicillin was performed using cefoxitin (30ug) disc diffusion method. Positive isolates were confirmed by Polymerase chain reaction (PCR) to detect the presences of mecA gene. Antimicrobial susceptibility of the isolates to various antibiotics viz: penicillin, erythromycin, clindamycin, gentamicin, kanamycin, amikacin, streptomycin, tobramycin, spectinomycin , tetracycline, refampin, teicoplanin, mupirocin linezolid, trimethoprim , trimethoprim sulfamethoxazole, ciprofloxacin, teigocycline, chloramphenicol and fusidic acid was determined using the disc diffusion method. Phenotypic detection of Macrolide; Lincosamide and group B Streptogramin ( MLS) was also performed. Susceptibility of the isolates to non antibiotic agents viz: ethidium bromide, cadmium acetate, and mercuric chloride was determined using disc diffusion method. Molecular characterization of the isolates to determine the clonality was performed using Pulsed Field Gel Electrophoresis (PFGE). Ddetection of PVL genes was accomplished by using PCR. The isolates were further subjected to typing based on SCCmec gene and ccr gene complex using a multiplex PCR. Results: Prevalence of MRSA was calculated taking into account 56 MRSA isolates identified from a total of 246 S. aureus recovered during the period of May - December, 2011 giving a prevalence rate of 22.8%. The other 23 MRSA isolates were not included in the prevalence study since no data relating to the total number of S. aureus recovered during March-April, 2011 was available, but they were subjected to molecular typing and characterization. Cefoxitin disc diffusion screening test was found to be 100% sensitive for detection of MRSA. As many as 53/79 (67%) of the isolates were CA-MRSA while 26/79 (32.9%) were HA-MRSA. A large majority 33/79 (41.8%) of the isolates were resistant to B-lactam antibiotics only; while 9/79 (11.4%) were multi-resistant. Erythromycin and clindamycin resistance were more in HA-MRSA compared to CA MRSA (50% vs. 18.4%; p<0.05) and (46.2% vs. 13.2%; p<0.05) respectively. The resistance profiles of HA and CA- MRSA were not significantly different in respect of rest of the antibiotics. All the isolates were resistant to mercuric chloride, while 86.1% were resistant to ethidium bromide and cadmium acetate. As many as 35/79 (44.3%) of isolates carried PVL genes of which the highest majority of isolates were CA-MRSA causing skin and soft tissue infections (17/35 (48.6%)). Molecular typing revealed that the majority 63/79 (79.7%) of the MRSA harbored SCCmec type IV and ccr type 2 both in the hospital and community. SCCmec type II and I were detected only in HA strains. PFGE yielded 20 major types and 15 subtypes of MRSA. Nineteen (24.1%) isolates belonged to the major and most predominant pulsotype 1, and another 10 (12.7%) to its different subtypes. All isolates of pulsotype 1 and its subtypes carried the SCCmec type IV. Conclusion: The study demonstrated that a fairly high percentage of the S. aureus isolates at SQUH were MRSA. Majority of MRSA, either HA Or CA-MRSA were not resistant to multiple classes of antibiotics. Most of CA-MRSA as well as the HA MRSA isolates carried SCCmec type IV genes. A large majority of the CA and HA MRSA isolates belonged to pulsotype 1 indicating the spread of a single clone in both the settings, a trend which is being reported from different parts of the world.