The present method of characterizing Vibrio parahaemolyticus strains involves serotyping or detection methods based on assessment of the presence or absence of genes thought to be markers of an organism's pathogenicity. It is unclear whether these assays detect all pathogenic V. parahaemolyticus strains since a clear correlation between the presence of a particular gene and the organism's pathogenicity has not yet been observed. We have described a proteomics-based method to distinguish individual V. parahaemolyticus strains on the basis of their protein profiles and identified a specific protein that is characteristic of the pandemic O3:K6 strain and its clonal derivatives. In the pandemic clone of V. parahaemolyticus, a histone-like DNA-binding protein, HU-alpha, has a C-terminal amino acid sequence different from those of other strains of V. parahaemolyticus. Upon further study, it was discovered that the gene encoding this protein has a 16-kbp insert at the 3' terminus of the open reading frame for this protein. By using the protein sequence of the unique biomarker for the pandemic clone of V. parahaemolyticus, it was possible to rationally design specific PCR-based probes and assays that permit the rapid and precise identification of pandemic strains of V. parahaemolyticus.