The clonal relationships and antimicrobial resistance of Staphylococcus aureus isolates from three fresh Minas cheese production lines were investigated. Putative S. aureus were confirmed by 16S rRNA gene sequencing and were characterised by multilocus sequence typing (MLST) and antimicrobial susceptibility. Overall, 33 out of 64 samples were contaminated with S. aureus (51.6%). The contamination rates of the dairies were 60.8%, 21% and 68.2%. Thirty representative isolates were selected to be typed by MLST and five sequence types (ST) were found (ST1, 97, 126, 3531), including the new ST 3816. The clonal complex 1 (CC1) was dominant. Resistance to commonly used antimicrobials was observed but only one strain was resistant to methicillin. This methicillin resistant S. aureus strain belonged to the CC126 that is commonly associated with mastitis in ruminants. The dissemination of zoonotic bacteria through the food chain is not a frequent event but represents a concern to public health.