Aim:The present study was undertaken to type Staphylococcus aureus isolates from cattle and buffalo mastitic milk on the basis of spa (X-region) and clfA genes, both responsible for producing virulence factors.Material and Methods:In the present investigation S. aureus isolates were isolated as per standard protocols. Typing of S. aureus was carried out by molecular detection of spa and clfA gene by polymerase chain reaction.Results:All the 32 isolates from cattle (16) and buffalo (16) were divisible into seven spa types with amplicon sizes ranging between 120 and 380bp. The cattle isolates produced seven different spa amplicons of 120, 150, 200, 250, 280, 300, and 330 bp with 3, 4, 6, 8, 10, 11 and 12 number of tandem repeats, respectively whereas buffalo isolates were divisible into five spa types with amplicons of 150, 200, 250, 330 and 380 bp having calculated number of repeats of 5, 7, 9, 12, and 14, respectively. Of the total isolates, 24 were considered pathogenic on the basis of more than seven number of tandem repeats. In the present investigation, clfA gene was amplified in 27 isolates from cattle and buffalo producing two different amplicons of 900 and 1000 bp sizes showing polymorphism. The most (71.80%) of the isolates produced amplicons of 900 bp while amplicon size of 1000 bp was produced by four (12.5%) of the isolates.Conclusion:The presence of these genes with a wide degree of polymorphism confirmed the pathogenic potential of S. aureus and their association with clinical manifestations in mastitis among cattle and buffalo.