Staphylococcus aureus is a major pathogen in ruminant mastitis. Staphylococcal mastitis in ovine hosts is remarkably variable in terms of acuteness and ranges from subclinical to gangrenous mastitis. S. aureus factors involved in such variations are still poorly documented. This study aimed at identifying the staphylococcal factors responsible for the acuteness of the infection. Two S. aureus strains, isolated from gangrenous (O11) or subclinical (O46) ewe mastitis, were selected for this work. Despite a close phylogenetic relationship, these strains were shown to reproducibly induce severe (O11) or mild (O46) symptoms in experimental ewe mastitis. Several omic approaches were combined to compare these two strains. Both strains were fully sequenced and their transcriptome and proteome were analyzed in culture conditions mimicking mastitis context. Results showed that dramatic differences between O11 and O46 rely on their ability to adapt to and to express their virulence in a mammary context rather than in their gene content. This study highlights differences in the expression of genes related to mobile genetic elements (especially prophages), the expression of genes involved in iron acquisition and metabolism, of transcriptional factors (SigmaB and SigmaS) and in exoprotein production. Serological Proteome Analysis (SERPA) showed that most of these exoproteins are indeed produced during mastitis. Analysis of 10 other S. aureus strains, focused on two of these exoproteins –SspB and a protein of unknown function- showed SspB is produced only in strains isolated from severe mastitis and the protein of unknown function in strains isolated from subclinical mastitis. The exact role of the genes identified here (exoproteins, mobile genetic elements, iron metabolism and acquisition) in the infection and in mastitis acuteness remains to be determined. Finally, we showed that O11 is transformable and can thus be subjected to mutagenesis. The genes identified here represent excellent candidates for targeted studies of the molecular basis of S. aureus pathogenesis in ruminant mastitis.