Staphylococcus aureus is an important pathogen causing skin and soft-tissue infections, systemic infections and toxemic syndromes. In order to have adequate information for treatment of S. aureus infections, it is important to understand trends in the antibiotic-resistance patterns as well as clonal identities across geographical regions. A total of 297 non-duplicate S. aureus isolates (209 clinical, 84 carrier and 4 environmental) were characterized by phenotypic and genomic methods. Antimicrobial susceptibility testing was performed by disk diffusion and the automated VITEK-2 system. PCR was used to amplify genes for accessory gene regulator (agr); capsular polysaccharide (cap) 5 and 8, exfoliative toxins (eta and etb), the toxic shock syndrome toxin- 1(tst) and Panton-Valentine Leukocidin (PVL). Typing of isolates was by the staphylococcal protein A (spa) typing. High level resistance was observed against penicillin and ampicillin (97.3%); trimethoprim/sulfamethoxazole (80%) and tetracycline (17.5%). Azithromycin, clarithromycin, erythromycin, clindamycin, linezolid, vancomycin, nitrofurantoin, fusidic acid, mupirocin and rifampicin recorded 100% activity against the isolates. Ninety-five percent of all strains (n=281) harboured the β-lactamase (blaZ) gene and 2.7% (n=8) possessed the mecA gene. The methicillin resistant S. aureus (MRSA) strains were resistant to at least 10 antibiotics including all penicillins, penicillin/penicillinase inhibitor combinations, carbapenem and cephalosporins. The staphylococcal cassette chromosome mec (SCCmec) typing of MRSA strains detected only SCCmec types I and IV in two strains (Y260: type I and Y59: type IV). The eta and tst genes were present in 0.7% (n=2) and 1.7% (n=5) of S. aureus isolates respectively. A high prevalence of PVL genes was noted in clinical isolates (79.4%; n=166); carrier isolates (56%; n=47) and environmental isolates (75%; n=3). The PVL protein was expressed in vitro by 68.5% of strains harboring lukS-PV and lukF-PV gene. All strains carried either the cap8 (91.9%; XX n=273) or cap5 locus (7.7%; n=23) while one MRSA strain was untypeable. A Single agr allele was detected in each S. aureus isolate with the majority in agr-2 (73.4%; n=218). Thirty-seven spa types were identified; predominant spa types among the methicillin-susceptible S. aureus (MSSA) were t084 (65%), t2304 (4.4%) and t8435 (4%). Prevalent spa types in MRSA were t002, t008, t064, t194, t8439, t8440 and t8441. Eleven novel spa types (t8435, t8436, t8437, t8438, t8439, t8440, t8441, t8442, t8952, t8953, t8953) were identified. The pT181 plasmid was successfully used to confer tetracycline resistance in S. aureus strains A56 and Y1. The use of phenotypic and molecular methods in this study provided useful information on antibiotic resistance and genetic diversity of S. aureus isolates from Ogun and Lagos States of Nigeria. The information provided could help in monitoring the evolution of S. aureus strains in Nigeria over time.