Staphylococcus aureus is recognized as a major etiological agent of the most important udder disease; mastitis. The virulence potential of S. aureus isolates is attributed to a combination of extracellular factors and invasive properties that are controlled at the genomic level. In this study molecular variations were studied among the 128 S. aureus isolates obtained from the mastitic crossbred cattle. The polymorphic patterns of protein A, coagulase, and IG genes were studied in the isolates using the PCR and PCR-RFLP methods. In addition, presence of other virulence genes responsible for the expression of adhesins and toxins was also screened. A considerable genetic variation was observed in amplified fragment of SPA, IG and CLF genes. The PCR-RFLP of COA gene yielded five different patterns. Occurrence of EBP, ENO and FNBA was found to be common in both high and low virulence isolates. However, the prevalence of FNBB and toxin genes was higher in clinical than subclinical isolates. The distribution proportions of adhesin genes EBP, FIB, FNBB, CNA, BBP, MAP CAP5, and CAP8 were 60.2, 59.4, 21.9, 6.3, 5.5, 80.5, 56.3, and 22.7%; for AGR I, II, III, and IV were 44.5, 32.8, 12.5, and 10.2%; and for toxins genes HLB, SEB, SEC, SED, SEE, SEG, and SEI were 82.0, 3.1, 5.5, 3.9, 0.8, 16.4, and 55.5%, respectively. The proportions of FNBB, EBP, FIB, HLB, BBP, SEG, and SEI genes were observed more in clinical cases. The significant genetic variations in SPA, COA, IG, and CLF genes were useful to differentiate the isolates that might be valuable for mastitis reduction programme.