Identification of the emerging pathogen Vibrio vulnificus biotype 3 has become a challenge for clinical laboratories in the last few years. In this study, the abilities of five commercial systems to identify this new species have been evaluated for the first time, using a unique collection of strains. Fifty-one well-documented wild strains of V. vulnificus biotype 3 were processed using API 20 NE, GNI+ Vitek 1 cards, ID-GNB Vitek 2 cards, Neg Combo 20 Microscan panels, and NMIC/ID-5 BD Phoenix panels. The numbers of strains identified as V. vulnificus by ID-GNB, NMIC/ID-5, and GNI+ were 50 (98.0%), 46 (90.2%), and 7 (13.7%), respectively. Neg Combo 20 Microscan panels and API 20 NE were unable to identify any of the strains of this emerging pathogen to the species level and mostly misidentifies them as other species of the Vibrionaceae family. Data on the phenotypic pattern of V. vulnificus biotype 3 when processed in all five systems as presented here could help clinical laboratories in identifying this new pathogen.