Staphylococcus aureus is involved in human and animal infections. Because of mastitis in dairy cows, milk can be contaminated by enterotoxin-producing strains, which constitutes a food poisoning risk. Animal handlers can be asymptomatic carriers, becoming an additional source of contamination. This research aims to improve our understanding of Staphylococcus aureus in small-scale dairy systems in central Mexico. Samples were taken in 12 dairy farms and included composite milk (from the four teats) and hand swabs from each farmer. Of 149 presumptive S. aureus isolates, 102 (84 from cows; 18 from farmers) were accurately identified by molecular methods. The genetic variability of 43 randomly selected isolates was determined by RAPD-PCR, and of these, 38 were genetically distinct (≤90% similarity). Of the 38 distinct isolates, 78.9% harboured at least one enterotoxin-encoding gene ( staphylococcal enterotoxin a ( sea )– sed , seg , and/or sei ), whereas 100% carried icaA – icaD genes and 28% carried the bap gene. The latter three genes are all involved in biofilm formation. Susceptibility to antibiotics, bacteriocins, and bacteriophages, was also assayed; 36.8% of isolates were resistant to penicillin G. Only five isolates were resistant to bacteriocins nisin A and AS-48, and phiPLA-RODI was the most effective bacteriophage, infecting all of the isolates. These results support the need to adopt management strategies to improve hygiene and milking practices in order to enhance herd health and diminish the risk of food poisoning associated with the consumption of raw milk cheese.