In the present study twenty five human urine samples of hospital patients were screened for Staphylococcus aureus. Twenty percent of the samples were positive for Staphylococcus aureus as yellow colonies were observed aerobically on mannitol salt agar, out of the five isolates two were catalase positive. On the basis of resistance against methicillin, out of the three catalase positive isolates, two were MSSA and one was MRSA. One MRSA and one MSSA strain was examined using PCR technique, for gene identification. The mecA and nuc gene were amplified using PCR technique. The presence of mecA gene and nuc gene in MRSA and MSSA respectively, confirmed the strains. Comparative gene analysis of mecA gene and nuc gene was performed using BLAST and CLUSTALW tools. Thereafter rooted phylogenetic tree was obtained for both mecA and nuc gene sequences explaining the genetic evolutionary lineage. Present study analyzed the resistance mechanism of MRSA and to identify the gene responsible in order to control the re-emerging methicillin resistant Staphylococcus aureus infection.