The Staphylococcus aureus is the most common isolated microorganism in ruminant animal species diagnostic with clinical or subclinical mastitis. Dairy herds with these diseases can transfer S. aureus into the milk supply, which can lead to food poisoning in humans. The objective of this study was to evaluate the profile of antimicrobial susceptibility, the presence of femA gene, the genetic relationships among isolates of S. aureus obtained from milk originating from flocks diagnosed with subclinical mastitis in nine rural properties in the northern of Minas Gerais State. To this end, 498 samples of bovine milk tested positive for the California mastitis test (CMT) were subjected to morphological methods and biochemical patterns for microbiological presumptive identification of S. aureus. The PCR test with the genetic marker femA was used to confirm the species S. aureus. All the 26 isolates presumptively identified as S. aureus amplified a fragment of 132 bp corresponding to the femA gene. The profile of antimicrobial susceptibility was performed according to the disk-diffusion methodology and two isolates were susceptible to all the antibiotics tested. The drug multiresistence was found in 80.76% of the isolates. The determination of the genetic profile and the clonal relationship among the isolates was performed by the method of DNA RAPD-PCR polymorphism. The S. aureus isolates were divided into two groups with 26 distinct subgroups. The analysis of RAPD-PCR showed no genetic diversity among them, heterogeneous profile and absence of clonality.