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In this study Staphylococcus aureus isolated from milk of the cow with bovine mastitis were used for screening the production of exoproteins, presence of enterotoxin genes and comparison of pathogenic strains which can aid in better understanding of evolution of virulence factors among the species and also in developing the specific vaccine against the S.aureus infection. In this investigation exoproteins like alpha and beta toxins were screened by hemolysin test, PCR technique was used for the molecular identification of S.aureus using 23S rRNA gene, detection of enterotoxin gene such as Staphylococcal enterotoxin a (Sea), Staphylococcal enterotoxin b (Seb) and comparison of pathogenic isolates was carried out by PCR-RAPD technique which was found to be 87.50% polymorphism.