Staphylococcus aureus is a causative agent of bovine mastitis, posing significant challenges to animal health and dairy productivity due to its genomic adaptability, diverse virulence, and antimicrobial resistance. This study investigated the genomic diversity, virulence potential, antimicrobial resistance determinants, and plasmid replicon types of eight S. aureus isolates associated with subclinical bovine mastitis in 50 cows on a single farm in South Africa’s Dr Kenneth Kaunda District.