Abstract : The appearance isolates of methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant S. aureus (VRSA), as well as vancomycin-intermediate S. aureus (VISA), in the community, becomes a big concern in worldwide public health in both developed as well as developing countries. Hence, the purpose of the current research aimed to examine phenotypic and genotypic detection of virulence factors in MRSA and VRSA and the frequency of VRSA and VISA isolates among conjunctivitis infections. The results showed that 6 (9.37%) of isolates were capsulated S. aureus by India ink staining, hence 67% of isolates showed the protease enzyme production. The results revealed that 57.8% of S. aureus isolates changed the color of DNase agar from blue to pink or rose, indicating that they were positive result. The results showed that 76.5% of S. aureus isolates produced gelatinase enzyme. The molecular results showed that all of S. aureus isolates do not contain the cap5 gene, while cap8 gene detected in 35% of S. aureus isolates. Also, result pointed out that 50% S. aureus of investigate isolates contained the hla gene. The findings of the molecular revelation of the nuc gene showed that 70% of S. aureus isolate gave positive for nuc gene.