Staphylococcus aureus is one of the most frequent agents causing hospital infections. S.aureus has a great ability to adapt itself to variety of conditions and successful clones can be epidemic and even pandemic by its ability spread from one continent to another. The aims of this study were to detect spa types of 397 methicillin-resistant S.aureus (MRSA) strains isolated from 12 centers in different geographical regions of Turkey from 2006 to 2008, and to investigate their clonality by PFGE and MLST typing. Additionally, 91 MRSA from four of those 12 centers isolated during 2011 were also studied for their spa types. PFGE profiles indicated the presence of a major pulsotype, namely pulsotype A with a rate of 91.4% (363/397), followed by pulsotype B (n = 18, 4.5%) and pulsotype C (n = 11, 2.8%). Among isolates tested 363 (91.4%) were SCCmec type III, 30 (7.6%) were SCCmec type IV. Sequence analysis of representative isolates revealed that ST239 (85.1%) was the most common MLST type followed by two MLST types ST737 (4%), and ST97 (2.8%), both SCCmec type IV. Two isolates were ST80 with SCCmec type IV. Of 397 isolates, 338 (85.1%) were t030, followed by t005 (2.5%) and t632 (2%). Among MRSA isolated during 2011, 64 (70.3%) of 91 were t030, 4 (4.4%) were t005, 2 (2.2%) were t015, and 2 (2.2%) were t1094. Among centers the t030 prevalence of 2006-2008 isolates ranged from 59-100%. The highest t030 prevalence was found in Ankara (100%) and lowest in Trabzon (59%) provinces which are located at central and northestern Anatolia, respectively. In Istanbul province, the prevalence of t030 was 94.5% among 2006-2008 isolates which decreased to 55.5% among 2011 isolates. Also a decrease in t030 rates was observed among samples from Konya and Trabzon but not from Aydin. Our results showed that the most common MRSA clone in Turkey is ST 239-SCCmec type III, t030 which persisted during the six years of the study period. Presence of PVL toxin gene was tested by PCR and 5 (3%) isolates found to be positive, of them two were SCCmec Type IV-ST80 and three were SCCmec Type III-ST239. This study is the largest epidemiological survey ever done in Turkey which showed presence of a hospital Turkish clone TR09 (ST239-SCCmecIII-t030) and a community clone TR10 (ST737-SCCmecIV-t005) largely disseminated in Turkey.