Staphylococcus aureus is a major pathogen associated with significant public health risks due to its virulence factors and antibiotic resistance. This study investigates the prevalence of virulence and antimicrobial resistance genes in S. aureus isolated from traditional dairy products in Kut, Iraq, a region with limited data on such contamination. A total of 100 dairy product samples (buffalo cream, buffalo milk, cow milk, and sheep milk cheese) were collected and analyzed. S. aureus isolates were identified using biochemical tests and confirmed by PCR targeting the nuc gene. The presence of blaZ, clfA, pvl, and mecA genes was evaluated, and antibiotic susceptibility was determined using the disk diffusion method. Out of 100 samples, 31 bacterial isolates were recovered, with 27 confirmed as S. aureus through nuc gene amplification. Among the total dairy samples, S. aureus was detected in 12 out of 36 cow milk samples (33.3%), 6 out of 16 buffalo cream samples (37.5%), 6 out of 31 sheep milk cheese samples (19.4%), and 3 out of 17 buffalo milk samples (17.6%). Genetic analysis revealed that 10 isolates (37%) carried the mecA gene, 7 (25.9%) harbored blaZ, and 4 (14.8%) were positive for clfA. None of the isolates tested positive for the pvl gene. Antibiotic resistance profiling indicated high resistance rates to erythromycin (74%) and penicillin (63%), while no resistance was observed to vancomycin. This study highlights the alarming prevalence of multidrug-resistant S. aureus in dairy products, particularly the high rates of mecA and blaZ genes, which pose significant public health risks. The findings underscore the urgent need for improved hygiene practices, antibiotic stewardship, and continuous monitoring of resistance patterns in dairy production to ensure food safety and protect public health.