Staphylococcus aureus is commonly involved in food poisoning due to production of toxins responsible for causing animal and human diseases. In this study, 60 strains of presumptive S. aureus isolates from raw milk and cheese were biochemically identified in four dairies: 54 (90%) from refrigerated raw milk (RRM) with counts exceeding 10 6 CFU/mL, and six (10%) from cheese with similar concentrations of CFU/mL. Out of the 60 strains of presumptive S. aureus, 46 (76.7%) amplified the femA gene and then they were investigated regarding the presence of the Toxic Shock Syndrome Toxin-1 (TSST-1) gene and the classical enterotoxin genes (SEs) types A, B, C, D and E: 31 (67.4%) carried one or more encoding toxin genes, and 13 different genotypes were identified. Twenty-one strains (61.8%) carried one gene; three (8.8%), two genes; seven (20.6%), three genes; two (5.8%), four genes; and one (3%), five genes. The sec gene was the most frequent one, followed by seb and tst. The sed gene was expressed by 10 strains (29.4%), sea by five (14.7%) and see by three (8.8%). The S. aureus isolates showed genetic potential for producing toxins of importance for public health that presented a danger of food poisoning.