In this study, the biodiversity of Coagulase-Negative Staphylococci (CNS) strains isolated in France from cheese related samples (227 isolates) and dry sausage related samples (204 isolates) was compared to the biodiversity of 297 clinical isolates. Species identification was performed using different molecular methods (specific PCR, "Staph array" hybridization and sodA gene sequencing). Infraspecific biodiversity of strains belonging to the main CNS species found in both food and clinical samples was then assessed by pulse-field gel electrophoresis (PFGE). For food-related samples, the main species encountered corresponded to Staphylococcus equorum (28.5%), S. xylosus (28.3%), S. saprophyticus (12.5%) and S. succinus (7.7%); while, for clinical isolates, the main species encountered corresponded to S. epidermidis (69.4%), S. capitis (9.8%), S. hominis (4.5%), S. warneri (4.5%) and S. haemolyticus (3.8%). The two main species common to both food and clinical samples corresponded to S. epidermidis and S. saprophyticus. Concerning infraspecific biodiversity, PFGE profiles of S. equorum, S. saprophyticus and S. epidermidis showed a large genomic biodiversity. Comparatively, S. xylosus exhibited a lower biodiversity. No correlation could be observed between PFGE patterns and either the geographical origin or the sample type. This study highlighted that no food strains had similar PFGE profiles to clinical ones and that the two main food-related species, S. equorum and S. xylosus, were not found in clinical samples. The identification of CNS species and the characterisation of the genetic diversity of the strains constitute a first step towards CNS safety assessment.