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Unveiling the molecular identity of the clinical strains implicated in human skin pathogenesis is being a mandatory task from epidemiological point of view and combating the emergence of multidrug resistance phenomenon. The present work underlines a molecular study on eighteen Staphylococcus aureus MRSA clinical strains (HA-associated MRSA) isolated from human skin lesions, consulted by dermatologist at Al-Qasim General Hospital, Imam Al-Sadiq Hospital, Babil Governorate, Iraq, using 16S RNA gene sequence analysis and PCR detection of the virulence genes mecA and tst-1. The suspect clinical strains, isolated from the human skin lesions on blood agar, showed typical Staphylococcus aureus features as follow: catalase positive, coagulase positive, golden yellow colonies on mannitol salt agar, and characteristic S.aureus profile on APISTAPH kit and VITEK2 system. All S.aureus clinical strains under study assigned as MRSA strains, deduced from their pattern of methicillin resistance. The 16S RNA sequence analysis of six MRSA strains, randomly selected, confirmed their affiliation to S.aureus. The occurrence of the two virulence genes mecA and tst-1 in all S.aureus MRSA clinical strains under study was 100 and 100 %, respectively as inferred from the banding pattern of PCR amplification of partial fragments of 855 and 326 bp, respectively using gene specific primers. The present finding would greatly underpin the predominance of S.aureus MRSA clinical strains among hospitalized patients with skin lesions infection whilst, increasing sample size is recommended in prospective studies for further exploring the epidemiology of HA-MRSA strains in Iraq.