We examined the genomic diversity of 29 representative Vibrio parahaemolyticus strains based on amplified fragment length polymorphism (AFLP) and multilocus sequence analysis (MLSA). Several strains had indistinguishable AFLP patterns, suggesting high genomic similarity. Recombination detection methods and phylogenetic reconstructions based on the gene sequences of recombination/repair protein (recA), DNA gyrase beta subunit (gyrB), and phosphoglucomutase (pgm) revealed that recombination has occurred within the species V. parahaemolyticus. We suggest that homologous recombination is an important force in the evolution of V. parahaemolyticus.Key words: diversity, homologous recombination, Vibrio parahaemolyticus, AFLP, MLSAThe species Vibrio parahaemolyticus was described in the 1950s during food-borne gastroenteritis outbreaks in Japan that lead to hundreds of cases of diarrhoea associated with the consumption of raw fish. In 1980, V. alginolyticus was proposed as a new species to encompass biotype two of V. parahaemolyticus. Phenotypically these two species share many features in common. Of an array of more than 50 tests, only utilization of D-glucosamine, growth at 10% NaCl, and Voges-Proskauer differ between these species 1) . V. alginolyticus and V. parahaemolyticus share 67% DNA-DNA hybridization similarity (DDH), and 57% with the pair V. harveyi and V. campbellii 5,21) . In spite of the close relatedness between these species, genomic fingerprinting analyses, such as amplified fragment length polymorphism (AFLP) and rep-PCR, and multilocus sequence analysis (MLSA) clearly discriminate the bacterial strains and species 5,11,18,20) . Currently, researchers are able to identify their isolates through the internet using curated MLSA data of vibrios (http://www.taxvibrio.lncc.br/) 22,24) . Because V. parahaemolyticus includes both human and marine animal pathogenic strains 7) , identification at the strain level is crucial for pinpointing the widespread successful clones associated with human and animal health worldwide.Since 1990s pandemic strains of V. parahaemolyticus have emerged from a single clone (serotype O3:K6), associated with hundreds of cases worldwide. Previous pulsed filed gel electrophoresis (PFGE) data indicated that V. parahaemolyticus strains have a non-clonal population structure, possibly with recombination between strains giving rise to new epidemic clones 9,16,25,26) . However, it is not clear yet if recombination occurs in housekeeping genes of V. para-