Most clinical isolates of Vibrio parahaemolyticus produce a major virulence factor known as the thermostable direct hemolysin (TDH). TDH is encoded by the tdh gene which is localized into a genomic pathogenicity island (PAI). Most environmental isolates are described as tdh negative. Therefore the question arised as to whether environmental strains lacked a full pathogenicity island or if only the tdh gene was deleted. This work demonstrates that most environmental non-toxigenic isolates 53 of 66 (80%) lacked a full PAI when compared with clinical toxigenic strains. By PCR assays, Southern blot and sequence analysis a genetic region of 80 kbp between genes VPA1310-VPA1396 was demostrated to be missing from environmental strains. These results highlight the genetic dynamism of the Vibrio parahaemolyticus pathogenicity island region and suggest that new pathogenic strains could arise by horizontal transfer of the island between toxigenic and non-toxigenic strain types.