Vancomycin antibiotic is a well-known drug of last resort in the treatment of methicillin-resistant S. aureus (MRSA), but recent studies have shown the emergence of resistance to vancomycin and other antibiotics. This study determines the phenotypic and genotypic prevalence of vancomycin resistant S. aureus (VRSA) among clinical isolates in Zaria Metropolis. A total of 350 suspected Staphylococcal isolates from clinical specimens (blood, urine, high vaginal swab, wound swab, ear swab, urethral swab) submitted to the Medical Microbiology Unit of the selected hospitals in Zaria were collected for the period of 6 months. The antibiotic susceptibility profile of MRSA isolates were determined using disc diffusion method while the minimum inhibitory concentration (MIC) for vancomycin was determined using Etest® gradient method. PCR and sequencing were conducted on the isolates to molecularly detect the presence of mecA and van genes (vanA, vanB, vanC, vanD, vanR and vanXY). Phenotypic VRSA evaluation showed that 3.92% of S. aureus isolates were VRSA, 19.6% of isolates were VISA (vancomycin intermediate S. aureus) and 76.47% of isolates were VSSA (vancomycin susceptible S. aureus). Twelve (12) isolates that had vancomycin MIC range of 4-16 µg/ml were selected for genotypic evaluation of virulent genes. All isolates amplified with 16SrRNA signifying all are S. aureus. The result shows that 58% of the isolates harbors mecA gene, 25% of isolates harbors vanA gene, 67% vanB gene, 41.7% vanC, 58.3% vanD, 83.3% vanR and 83.3% vanXY. The presence of van gene was implicated in generation of Vancomycin resistance isolates.