120 milk samples (represent 35 cows) were randomly collected from different small holder farms, firstly tested for subclinical mastitis by CMT. 38 CMT positive samples were subjected for conventional methods of isolation and identificacion of Staph aureus. 6 isolates of Staph aureus were isolated which were subjected for genotypical characterization for the presence of clumping factor and coagulase genes by PCR assay using oligonucleotide primers that amplified genes encoding cluming factor (clfa)gene, and (coa)gene. The results of PCR assay revealed that 5 isolates of Staph aureus were positive for coagulase gene, while 2 isolates were positive for clumping factor gene. The chemical analysis of milk showed that there were significant statistical increase in total whey protein, albumin, sodium and chloride in cows' milk samples with subclinical mastitis. While, there was a significant decrease in both calcium, phosphorous and potassium levels in comparing with the normal milk. The present study was carried out to study the presence of some virulence factors genes in Staph aureus isolated from bovine subclinical mastitis which is very important prerequisites for implementation of effective control programs to face the economic losses due to subclinical mastitis caused by this microorganism.