This work evaluates whether isolation and toxicity of subgingival Staphylococcus aureus strains correlate with progression of periodontal lesions and whether isolates are characterized by a specific genomic background. The study involved 165 subjects affected by generalized aggressive periodontitis. Three sets of samples of supragingival and subgingival plaque were obtained at 45-day intervals from active and non-active sites, to detect S. aureus . Susceptibility to antibiotics, the presence of 17 genes, genomic restriction profiles and multilocus sequence typing (MLST) were performed to characterize all isolates. S. aureus was detected in 37.6% of the subjects. Subgingival colonization rates were 66.1% and 12.9% for active and non-active sites, respectively ( P <0.01). Supragingival and subgingival isolates were shown to be distinct by molecular genotyping and DNA fingerprint analysis. MLST showed that isolates were not genetically related and no sequence type was predominant in any of the two locations. These data demonstrate that S. aureus is associated with the progression of aggressive periodontitis and that a specific set of characters is necessary for the bacterium to colonize subgingival sites. Comparative analysis of genomic structure and genetic-related data suggest that the periodontal environment could promote genetic evolution of strains.