The study was aimed to determine and characterize the nasal carriage rate of S. aureus among apparently healthy farm animals including cattle, sheep, and goats using traditional and molecular characterization. The study was conducted in Duhok province during the period from November 2021 to March 2022. Furthermore, the isolates were screened for the presence of MRSA using the standard Kirby-Bauer disk diffusion method (oxacillin discs) and genotypically by PCR targeting the mecA gene. Among the 300 tested nasal swabs, 209 (69.7%) samples were positive for S. aureus isolation using traditional methods. The isolation rate was 62.7% (47/75), 66.7% (100/150), and 82.7% (62/75) in cattle, sheep, and goats, respectively. Amplification of species-specific nuc gene confirmed that 119 of 209 (56.9%) animals carried S. aureus in their nasal cavity. The isolates showed variation toward different antibiotics used in this study and the highest resistance rate was recorded toward penicillin at a ratio of 72.3% (86/119). This study confirms the occurrence of MRSA for the first time in nasal swabs from a healthy animal in Duhok Province. The MRSA isolates were found only in cattle (7/119) and none of the nasal carriages isolates from sheep and goats were carried MRSA isolates. The presence of MRSA and multidrug-resistant MRSA among healthy cattle could be considered as a potential reservoir for transmission of multidrug-resistant MRSA to humans especially farm workers and they could act as a reservoir to spread MRSA in livestock. Further studies are required for a better understanding of pathogenic transmission and for confirming the origin of the strains, whether are of human origin or vice versa.