Staphylococcus aureus is a widespread opportunistic pathogen that can cause food-borne illness and is sometimes associated with raw milk and raw milk cheese products. The traditional taxonomic procedures for classification of staphylococcal species are time consuming and often several tests are required. FTIR spectroscopy offers a rapid method for the discrimination and identification of S. aureus strains isolated from raw milk and raw milk cheeses. FTIR spectroscopy was used to discriminate S. aureus from other species of Staphylococcus. This was achieved by using a model composed of 39 species and subspecies of Staphylococcus. The model was validated using a set of spectra of strains isolated from raw milk and different varieties of French raw milk cheese. S. aureus was successfully discriminated from the other species of Staphylococcus and all the strains of S. aureus isolated from raw milk and different varieties of French raw milk cheese were also successfully identified as such. These results demonstrated that FTIR spectroscopy is a rapid (results obtained within 24 h starting from a pure strain or a single colony) and robust method for the identification of S. aureus isolates of dairy origin and food-borne origin in general.