The understanding of bacterial virulence and immune evasion mechanisms provide novel opportunities to adopt preventive measures and design therapeutics against most prevailing resistant and virulent strains. With this background, this study was designed to characterize Staphylococcus aureus, the most common pathogen,using conventional microbiological and molecular methods. The agar disc diffusion method was used to evaluate the antibiotic susceptibility. Virulence-associated genes were detected using PCR while association analysis was used to test the likelihood of strains carrying combinations of genes involved in toxin production and/or host immune evasion. Highest resistance was observed against beta-lactam group followed by cephalosporin, lincosamide, tetracycline, macrolides and aminoglycosides. No resistance was observed against vancomycin and linezolid. Among genes involved in host immune evasion, Staphylococcus protein A (spa) was identified most frequently (81%) and proportions of capsular polysaccharides (CPs8), clumping factor A (clf A) andintracellular adhesion A (ica A) were 78%, 68.5% and 40%, respectively. ica D and CPs5 could not be amplified from any isolate. Toxin genes were present in 43.5% isolates. Among toxin genes, enterotoxins (SEs) were most frequently detected followed by enterotoxin (ETs) (24.09 %) and toxic shock syndrome toxin (TSST-1) (15 %). More than one toxin genes were present in 32.5% isolates. In addition, cluster analysis indicated that host immune evasion and toxin genes were not associated with each other suggesting the presence of diverse lineage specific strains in sore throat patients. However, the intraspecific association was noticed among these genes. Coa and spa polymorphism and association analysis indicated that spa negative isolates possess Coa of 1200 and 900bp, whereas spa positive isolates contain Coa of 650bp and 750bp. The most prevalent genes, spa, CPs8 and sea may be considered as molecular targets in designing treatment and control strategies.