Staphylococcus aureus is a commensal organism of skin and nose in nearly 30% of human population produces a number of virulence factors like biofilm formation regulated by bap gene encodes for biofilm associated protein. In addition to Staphylococcus aureus efflux-mediated multidrug resistance gene smr. Three virulence genes were identified using conventional PCR on a total of 12 Staphylococcus aureus strains. The most commonly found virulence genes were nuc12/12 (100%), smr12/12 (100%) and bap10/12 (83.33%).Three of positive PCR products from each of S. aureus bap and smr genes were used for sequencing and phylogenetic analysis by using programs Bio Edit 7.0.4.1 and MUSCLE then Six nucleotide sequences for S.aureus isolates were produced and entered into GenBank using accession numbers OR344353 toOR344355 forbap gene, OR344356to OR344358 for smr gene, and showed almost typical amino acid sequences of S. aureus isolatesfrom bovine milk and dairyutensils, while human isolates showed major mutations through change and addition. The phylogenetic tree targeting bap gene formed four clades where all S. aureus isolates recovered from bovine milk and dairy utensils revealed a high degree of similarity to Staphylococcus epidermidis isolated from nosocomial infections in humans in Brazil and low homology with S. aureus isolate from bovinemilk in India. Also S. aureus isolate from human nasal swab in Egypt showed a high homology with S.aureus isolates isolated from bovine milk in India. Concerning smr gene, all S. aureus isolates from this study showed a high homology with S. epidermidis isolated from ovine milk in Italy.