This study was conducted for estimation of subclinical mastitis prevalence caused by Staphylococcus aureus (S. aureus) in apparent normal lactating ewes in the areas around Baghdad (Al-Rasheed, Al-Yousifya, Al-Latifya). 400 milk samples from 200 ewes were collected and examined by California mastitis test (CMT), Bacteriological examination was done by culturing on Blood agar, Mannitol salt agar, Staph-110 agar and Chrome agar then bacteria examined by Gram stain and biochemical test. Antibiotic sensitivity test and molecular assay by PCR were done to detect methicillin-resistant strains with the phylogenetic study. The results showed that 49/400 samples gave positive to CMT in the field and positive to S. aureus isolation. The percentage of subclinical mastitis in ewes was 12.25% in this study. All isolated bacteria were resistant to methicillin 100%. The result of PCR revealed that 16.32 % (8/49) of the MRSA were possess mecA gene, while no isolate carried the mecC gene, PCR-product for 8 positive samples of mecA target gene were sequenced, analyzed, and reported in Genbank-NCBI and obtained accession number and became a reference to Iraq and the Middle East and the world. Seven samples that match the global results by 100%, and one sample contains a mutation at the site 1539, Nucleotide. Our conclusion revealed that detection of subclinical mastitis in sheep very important caused by S. aureus and all S. aureus was resistant to methicillin and some strains possess mecA gene. However, absence of mec A in other MRSA isolates requires detecting the alternative genetic possibilities related to the resistance profile and fragment of gene used.