Staphylococcus aureus is a well-known commensal and pathogen agent of many wild and domestic animals. A wide variety of infections can be caused by S. aureus, from suppurative skin infections to life-threatening septicemia. This study was conducted to determine the prophage typing and the pattern of antibiotic resistance of S. aureus isolated from broiler poultry before they have been slaughtered. In this study, 200 nasal and cloacal swab samples from 20 different flocks were collected for bacterial isolation. Staphylococci were identified using biochemical and molecular methods before being examined for mecA gene detections in all samples resistant to oxacillin and cefotaxime. The highest value of antibiotic resistance was observed against ciprofloxacin (94%), and the maximum value of susceptibility was to gentamicin (85%). Twenty-eight (27%) samples were resistant to oxacillin. In methicillin-resistance Staphylococcus aureus (MRSA) isolates, 5 prophage types were observed, where the SGB prophage with a frequency of 75% was identified as a dominant prophage; in isolates of S. aureus susceptible to methicillin, 8 prophage types were observed, where SGFa prophage with a frequency about 82% was the dominant prophage. The high prevalence of MRSA isolates can indicate the risk of transmission of these bacteria to the food cycle. Furthermore, existence of various prophages in these isolates can be considered a threat to public health in producing pathogenicity factors in this bacterium while also empowering other bacterial pathogenicity, even other bacterial genera.