The objectives of the study were to check the occurrence of Methicillin-Resistant Staphylococcus aureus (MRSA) and the molecular characteristics of the isolates within the nasal carriage of healthy human, cattle and sheep. One hundred and fifty animal samples (100 from sheep, 50 from cattle) and 100 samples from humans in contact with animals were collected in the study. Human and animal nasal swabs samples were collected at Basateen slaughter house. The isolation and identification of S. aureus isolates were applied according to traditional biochemical tests. Disc diffusion test was performed to record resistance and MRSA isolates. PCR was done for detection of nuc, and mecA genes. Only 60 out of 250 nasal swab samples produced S. aureus (24%), and 10 of which were MRSA (16.6%). All S. aureus isolates were sensitive to vancomycin and resistant to oxacillin, cefoxitin and erythromycin.Two isolates from sheep nasal swabs were intermediate resistant to cefoxitin and ofloxacin (50%). All isolates were nuc gene positive, while two out of the 10 MRSA isolates (20 %) were mecA negative, whereas all, the methicillin sensitive S. aureus (MSSA) were mecA negative. Therefore S. aureus and MRSA from sheep, cattle and human are considered a potential risk for zoonotic transmission, this study drew attention to the credibility of the mecA gene and its usefulness in the detection of all MRSA strains without referring to the traditional methods.