One hundred and five isolates of Staphylococcus aureus were collected from different body sites and lesions of in and out patients from both sexes who attended Al-Kadhimyia teaching Hospital during the period from November-2012 until March-2013 for the isolation and identification of Staphylococcus aureus. Bacterial isolates were identified by subjecting them to the standard laboratory procedures and use of antibiotic sensitivity test to cefoxitin. The results showed that sixty isolates (57.1%) out of the total of one hundred and five were identified as methicillin resistant Staphylococcus aureus. The results showed that these samples were unevenly distributed to body sites and lesions with the wound swabs constituting the higher number of samples from which S. aureus was isolated while cerebrospinal fluid (CSF) stood for the least number. The results of the present study showed that bacterial DNA was extracted with a final concentration ranged from 4.9- 167.8 ng/l and a purity ranged from 1.17- 1.9. The results of the multiplex PCR amplification of the 16S rRNA gene showed that it was present in all the sixty isolates of MRSA (100%) with a PCR product size of 756 bp. Furthermore, PCR product size of 433 bp correspondent to the lukS/F-PV gene was detected in thirty (50%) of the isolates while thirty (50%) of the isolates showed negative results. It was shown that this mec A gene was successfully amplified (conventional PCR) in fifty seven out of the sixty MRSA isolates, with a product size of 1339 bp, resembling a percentage of (95 %) of the isolates while only three isolates (5%) lacked this gene and gave negative amplification results. Furthermore, conventional PCR of SCC mec type IV gene revealed that thirty nine isolates (65%) out of sixty had shown prominent amplification with product size of 450 bp. Whereas amplification did not occur in twenty one isolates (35%). In view of the molecular findings of this study, its clear that the sixty samples of MRSA were of main two types, namely the community acquired MRSA and hospital associated MRSA with a percentages of (65 %) and (35%) respectively. The community acquired MRSA was most frequently isolated from wound swabs (28.21%) while sputum samples with a percentage of (33.33%) created the main isolation source of the hospital associated type of MRSA. LukS/F-PV was detected in thirty out of the total sixty samples (50%) of both types (community and hospital associated MRSA) and SCC mec type IV gene was successfully amplified in thirty nine out of the total of sixty samples (65%) of both types (community and hospital associated MRSA). mec A gene has been detected in thirty seven out of a total of thirty nine samples and in twenty out of a total of twenty one samples of community and hospital associated MRSA, respectively