We performed Whole-genome sequencing (WGS) of six S. aureus strains isolated from Peshawar, Pakistan, was conducted in this present study to identify the possible pangenome of S. aureus. These strains were then compared with the 200 fully sequenced genomes and 27 draft genomes of S. aureus from Pakistan available in the PATRIC database. Bioinformatics studies involving sequence assembly, quality check, Multi-Locus Sequence Typing (MLST), and Cluster of Orthologous Genes (COGs) were performed to examine the genetic variations and the evolutionary patterns of these strains. The de novo assembly of the S. aureus genomes indicated the genome size to lie between 1. 6 to 2. 9 Mb with average GC percentage. MLST analysis identified diverse sequence types among SA1, SA2, SA3, SA4, SA5, SA6 isolates belong to ST 45, 30, 772, 1413, 30, 30 and carries no SCCmec, (mecA gene, SCCmec type V, VII, mecA), mecA, (SCCmec type IV, mecA, Iva), (SCCmec type IV, mecA, Iva). Using the pangenome analysis of the 200 S. aureus genomes, it found a total of 9, 118 genes while sharing 1, 620 core genes, 307 soft core genes, 1, 161 shell genes, and the remaining 6, 030 of cloud genes. Thus, this analysis reveals the fact that the pangenome of S. aureus is open, suggesting its ability to obtain new genes and adapt to the environment. The COG analysis showed the functional classifications of the genes underlying metabolic processes. These outcomes are crucial for clinicians and therapeutic strategies for treating bacterial S. aureus infections.