Staphylococcus aureus (S. aureus) is remarkable pathogen and causative agent of hospital acquired (nosocomial) and community acquired infections. S aureus can acquire resistance to most antimicrobial agents (antibiotics). A total 295 S aureus isolates were collected from two local hospitals from various sites of body patients, such as urine, pus, sputum, wound, and blood. Patients’ ages were ranging from 5-84 years from males and females. The number of identified S aureus was 83 detected by traditional and methods and confirmed by molecular method using 16S rRNA gene in polymerase chain reaction (PCR). Antibiotic sensitivity profile was performed to evaluate the resistant and sensitive strains and predominance of methicillin resistant S aureus (MRSA). A total 6 (7.3%) from all S. aureus isolates was MRSA. MRSA isolates were multi-resistant for all antibiotics, which used in the current study. Several genes that participate in antibiotic resistance were investigated. SasX gene was detected in 11 (12.3%) samples which was multi-resistant for many antibiotics. In addition, Furthermore, Exfoliative toxin C and D (etC and etD) genes. The etD gene was detected in 33 (39.75%) samples, but etC gene no detected in all of isolates. In addition, probiotic lactobacilli species (spp.) e.g. L acidophillus, and L reuteri against different isolates of methicillin resistence S aureus from different sites of infections observed variance in their inhibitory activity ranging from 9-17mm. In addition, lactobacilli spp. were collected from different sites and different results showed for S aureus in culture broth and cell free culture supernatant.