Staphylococcus aureus, particularly methicillin-resistant S. aureus (MRSA), is an important zoonotic pathogen which not only causes significant economic loss in livestock production but also emerges as a potential threat to public health. Compared with bovines, the information on the colonization of S. aureus and MRSA in yaks, the only bovine species providing meat and other necessities for Tibetans living at high altitude, is very limited. Therefore, in the current study, S. aureus and MRSA prevalence, virulence genes, and antibiotic and antiseptic resistance properties in yaks from 18 counties of Ganzi Prefecture, Sichuan province, China were investigated. The results revealed that the overall prevalence of S. aureus during yak breeding was 7.10% among 1281 samples (91/1281), containing 9.44% from nasal (62/657) and 4.65% from anus (29/624). Nearly all of the S. aureus isolates carried at least one staphylococcal enterotoxin (SE) gene and the predominant enterotoxin gene was selx (51.65%).In addition, virulence genes (hlα, hlβ, pvl, and tsst-1), antiseptic resistance genes (qacA/ B, qacC, and qacG), and heavy metal resistance genes (copA, arsB, cadD, and arsA) were also found. Furthermore, 24 MRSA strains were identified. SCCmec, spa, and multilocus sequence typing typing revealed that the predominant types of MRSA were ST59-IVa-t437 and ST59-III-t437. It was noteworthy that all these methicillinresistant strains were resistant to two or more antibiotics and possessed virulence genes. The minimal inhibitory concentration (MIC) values of antiseptic peroxyacetic acid, sodium hypochlorite, and benzalkonium bromide against these MRSA strains were measured and the MIC values of benzalkonium bromide (1.22-9.77 μg/mL) were relatively low. Furthermore, the challenge with 1/4 MIC of oxacillin sodium or ofloxacin or benzalkonium bromide for 216 h increased the resistance of the MRSA strain YB786 to these antibiotics but decreased the MIC value of benzalkonium bromide. The results provide an indication of the health risks associated with these S. aureus strains, especially methicillin-resistant strains from yaks and new approaches are needed to treat these strains.