Staphylococcus aureus (S. aureus) is one of the leading causes of human diseases in hospital and community settings. Methicillin resistant Staphylococcus aureus (MRSA) has emerged as a significant problem worldwide, resisting all known -lactam antibiotics, including penicillin and cephalosporins. Increased morbidity and mortality caused by MRSA have increased financial burden on healthcare systems worldwide. Information regarding the genetic diversity of MRSA in the Pretoria region of South Africa is limited. The relatedness of MRSA isolates has been reported in a previous departmental study, using staphylococcal cassette chromosome mec (SCCmec) and pulsed-field gel electrophoresis (PFGE). Staphylococcal protein A (spa) types, accessory gene regulatory (agr) groups and multilocus sequence types (MLST) were not reported. A total of 194 MRSA isolates were collected from the Steve Biko Academic Hospital in the Gauteng province (South Africa) from April 2010 to August 2011. This study analysed the isolates using spa, agr and MLST typing. The results for spa typing included 187 isolates as one of the isolate was contaminated (isolate 4) and six isolates were untypeable using spa typing. Twelve distinct clusters (A to L) were obtained. Cluster A had five subclusters (A1 to A5), cluster B had four subclusters (B1 to B4), cluster C and D had two subclusters each (C1 and C2 and D1 and D2, respectively), cluster E had four subclusters (E1 to E4), clusters G and K both had two subclusters (G1 and G2 and K1 and K2, respectively). Clusters F, H, I, J and L had no subclusters. The agr typing showed that majority of isolates belonged to agr group I [84.5% (163/193)] followed by agr group III [7.3% (14/193)], agr group II [4.7% (9/193)] and agr group I and III [3.6% (7/193)]. No agr group IV was detected. Ten representative isolates were selected for spa sequencing and MLST typing based on the PFGE results. The sequence types (ST) corresponded to three pandemic clonal complexes (CC), which have been reported worldwide spa type t012-ST36/CC30, spa type t037-ST239/CC8, spa type t891-ST22/CC22 and spa type t1257-ST612/CC8. The dominant pulsotype from PFGE typing (57%, 110/191) corresponded to pulsotype A and was represented by spa type t037-ST239. One Panton- Valentine leukocidin (PVL) positive isolate was detected and was identified as spa type t891- ST22/CC22. Combining different molecular techniques showed that typing assays, such as spa, agr and MLST typing can accurately be used to determine the genetic diversity of MRSA. Compared to PFGE typing, the three Polymerase chain reaction (PCR) based techniques were rapid and less labour intensive but MLST typing was more expensive. The spa types and sequence types identified in the study represent major clones that are disseminated in South Africa and worldwide. The detection of an epidemic clone [t891-ST22/CC22 (EMRSA-15)] harbouring the PVL gene as well as one of the most common pandemic clones [(spa type t037- ST239/CC8)] in this clinical setting is alarming. Results from this study emphasise the need for strict infection control policies to prevent possible outbreaks of these epidemic and pandemic clones that are already circulating in this clinical setting.