Rapid detection of sources and transmission routes by molecular methods provides key data for risk management of methicillin-resistant Staphylococcus aureus-induced infections acquired in both the community and hospitals. This study aimed to determine the clonal relationship of methicillin-resistant S. aureus strains isolated from our hospital by pulsed-field gel electrophoresis (PFGE) and Staphylococcal protein A (spa) typing methods and to identify the predominant clones in Cukurova Region, Turkey. All isolates analyzed by PFGE were distributed among 11 clusters. Clusters A (n = 19) and B (n = 27) were 84.1% similar and accounted for 61% of all samples. All isolates were distributed among 18 spa types, with the most common type being t030 with 31 isolates (41.3%), followed by t223 with nine isolates (12%) and t127 with seven isolates (9.3%). We found that t030 was the most common spa type in the area where the study was conducted, as also previously shown in studies undertaken in Turkey. However, the rate of t030 in our study was below the rates reported in the literature. We also detected some rare or sporadic spa types like t127, which has not been previously defined in our country. We consider that the spa typing and PFGE methods are useful for research on clonal relations in monitoring the changing prevalent clones in specific regions.