Key Points Although certain Enterococcus genus are used as starter cultures in many food products, this bacterial group is considered a human and animal pathogen which can cause nosocomical infections and urinary tract infections, and contribute to food spoilage. Accurate and reliable identification of Enterococcus genus present in food is of great importance for predicting shelf life and for managing and reducing microbiological food hazar. Phylogenetic trees obtained from MALDI-TOF MS and VITEK2 analyses were compared to evaluate the discriminative resolution of these two systems.