The present study aimed to isolate and identify Methicillin-Resistant Staphylococcus aureus MRSA from the nasal cavity of healthy cows and buffaloes and their breeders in Nineveh Governorate and detect some virulence factors by using molecular methods. A total of 150 samples of cotton swabs were collected randomly from different areas of Nineveh governorate. The samples were cotton swabs from the nasal passages of healthy cattle, buffaloes, and their breeders (50 swabs of each type). All the samples were subjected to culture and molecular testing. The results showed the highest isolation percentage of S. aureus from cattle followed by breeders, then buffaloes, at 54%, 40%, and 32%, respectively. The total isolation percentage of MRSA was 65.1%. The highest percentage was in buffaloes, followed by breeders and cattle, at 93.75%, 70%, and 44.44%, respectively. Out of 41 isolates from cattle, buffaloes, and their breeders, the virulence genes clfA, clfB, and coa were detected in MRSA at rates of 100%, 80.49%, and 65.85%, respectively. The current study concluded that cattle and buffalo are considered carriers and potential transmitters of MRSA, which makes them risk factors for infection in humans, especially those who are in direct contact with animals. Together, these findings also highlight the need to prevent the transmission of zoonotic pathogens to humans via occupational exposure or consumption of contaminated animal products.