Histamine poisoning is caused by the consumption of fish and other foods that harbor bacteria possessing histidine decarboxylase activity. With the aim of preventing histamine formation, highly specific mass spectral fingerprints were obtained from the 16 major biogenic amine-producing enteric and marine bacteria by means of MALDI-TOF MS analysis. All bacterial strains analyzed exhibited specific spectral fingerprints that enabled its unambiguous differentiation. This technique also identified peaks common to certain bacterial groups. Thus, two protein peaks at m/z 4182+/-1 and 8363+/-6 were found to be present in all Enterobacteriaceae species analyzed except for Morganella morganii. Peaks at m/z 3635+/-1 and 7267+/-2 were specific to both M. morganii and Proteus spp. Biogenic amine-forming Proteus spp. exhibited three genus-specific peaks at m/z 3980, 7960+/-1 and 9584+/-2. The genus Photobacterium also showed three genus-specific peaks at m/z 2980+/-1, 4275+/-1 and 6578+/-1. The two histamine-producing Gram-positive bacteria Lactobacillus sp. 30A and Staphylococcus xylosus exhibited a few protein peaks in the 2000-7000 m/z range and could be easily distinguished from biogenic amine-forming Gram-negative bacteria. Clustering based on MALDI-TOF MS also exhibited a good correlation with phylogenetic analysis based on the 16S rRNA gene sequence, validating the ability of the MALDI-TOF technique to establish relationships between microbial strains and species. The approach described in this study leads the way toward the rapid and specific identification of major biogenic amine-forming bacteria based on molecular protein markers with a goal to the timely prevention of histamine food poisoning.