Foodborne illnesses are caused by ingestion of contaminated food or water. Staphylococcus aureus is able to produce enterotoxins and is one of the most common agent responsible for outbreaks of food poisoning. Intoxication is due to the ingestion of preformed enterotoxins in the food contaminated by the bacteria, which may continue viable. Among the foods involved in staphylococcal food poisoning, the cheese stands out due to the fact that S. aureus is found both in raw milk and in manipulators. The objective of this work was to isolate, identify and molecularly characterize S. aureus isolated from the processing chain of organic and conventional Minas frescal type cheese. Samples were collected from six dairies in the State of São Paulo within a radius of up to 200 kilometers from Campinas, with two collections in each dairy. The following samples were collected: raw milk, pasteurized milk, manipulators, environment (equipment, utensil, floor) and final product in order to isolate the target bacterium. Afterwards, the samples were incubated in Baird Parker Agar (BP) and the characteristic colonies were isolated with subsequent biochemical tests and polymerase chain reaction (PCR) for the identification of S. aureus. After confirmation of the species, the enterotoxin encoding genes (sea-see, seg-sej) were investigated by PCR and subtyping of spatyping, agr type and pulsed-field electrophoresis (PFGE) were performed. Thirty-eight S. aureus were identified, 18 (47.36%) of organic dairy products and 20 (52.63%) of conventional dairy products. Among the 38 isolates, 34 isolates (89.47%) presented at least one enterotoxin producing gene, with seg in 25 isolates (65.79%), sei in 18 isolates (47.37%), seb in 7 isolates (18.42%), sej in 8 (21.05%), seh in 5 (13.16%) and no sea, sec, sed and see genes were detected.The agr I gene was found in 5 isolates (13.16%), agr II in 11 (29.0%), agr III in 17 (44.74%), agr IV in 3 (7.89%); it was not possible to identify agr in 2 isolates (5.3%). A total of 14 different spa types were identified, t021 was the most frequent type (8 isolates, 21.05%), t127 was found in 5 isolates (13.16%) and t1062 in 3 isolates (7.89%). Seventeen clusters were detected based on the PFGE technique, 1 cluster with 5 isolates, 1 with 4, 2 with 3, 4 with 2 and 9 with only 1. Of the 32 profiles 4 clusters presented 2 clones with similarity of 100%. The abundance of isolates was similar between conventional and organic dairy products. The results obtained in the PFGE corroborate the identification of the main transmission points of the S. aureus strains, such as brine, utensils (lira), raw and pasteurized milk used to produce Minas frescal cheese.