A total of 30 milking buffaloes, 3 to 5 years age, were randomly selected from farm of Faculty of Veterinary Medicine-Suez Canal University for investigation of Staphylococcus aureus subclinical mastitis by California mastitis test (CMT), culture method and Polymerase Chain Reaction (PCR). The detected cases were isolated and a controlling attempt was carried out prior and post milking processes. The total number of quarters affected by subclinical mastitis using CMT was 30 (29.41%) representing 18 buffaloes (60%). PCR is rapid technique for detection of Staphylococcal subclinical mastitis when compared with culture methods. S. aureus, was sensitive to ampicillin, amoxicillin, cloxacillin, gentamicin, amoxicillin + clavulinic acid, oxytetracyclin and pencillin G. After application of control program for one month, the cure rate was 25% as evaluated using culture methods and 36.36% as evaluated using PCR assay. From the economic point of view and diseases control, it could be recommended that culling of dairy buffaloes suffering from Staphylococcus aureus subclinical mastitis that did not respond to treatment is a better choice, also the caution and restricted prescription is recommended to avoid development of resistant bacteria and to avoid antibiotic residues in milk.