Staphylococcus aureus is one of the major causes of community and hospital acquired infections. As well as bacteriophage considered as a major risk factor acquires S. aureus new virulence genetic elements for it.  A total number of 119 S. aureus isolates obtained from Riyadh Military Hospital. And were studied for phage typing and the incidence of toxin genes by PCR. Methicillin Resistant S. aureus isolates (MRSA) indicated high special prevalence of phage group II with a highly increase for phage type Ø3A compared to MSSA. Phage group II on Methicillin Sensitive S. aureus isolates (MSSA) considered an epidemiologic marker with frequent strong reaction compared to group III and phage group I. Phage type Ø75 may play an important role in a combination with Ø80 or/ Ø81 by having PVL toxin to be CMRSA lineages. 68% of S. aureus isolates had toxins. The most prevalent toxins were SEO, in 50.8% in MSSA & 25% in MRSA isolates. SEI was detected in 40.3% in MSSA & 29.1% in MRSA isolates. Also, SEA was 28% in MSSA & 33.3% in MRSA isolates. Phenotypic and genotypic variations between MSSA isolates seemed to be horizontally, while in MRSA isolates were vertically. It was obvious that five toxins together were located in more than one isolates in MSSA.