Vibrio parahaemolyticus is a major cause of foodborne gastroenteritis in China, Japan, and other countries. The pandemic O3:K6 clone, which harbors thermostable direct hemolysin [tdh] gene and toxRS/new gene, is mainly responsible for the foodborne outbreaks after 1995. Previous studies showed that genes in the pathogenicity island-1 (VPaI-1) and VPaI-5 are harbored only by pandemic strains, whereas genes in VPaI-7 and type III secretion system 2 are closely associated with tdh-positive strains of V. parahaemolyticus. In this study, we examined the distribution of genes encoding VPaI-2, VPaI-3, VPaI-4, VPaI-6, type VI secretion systems (T6SS), biofilm, and type I pilus in 71 food and 116 clinical strains of V. parahaemolyticus. The results showed that most of the pandemic strains of V. parahaemolyticus harbored the complete genes of VPaI-2, T6SS, and type I pilus. In contrast, most of the pathogenic strains (harboring tdh gene or TDH-related hemolysin [trh] gene) and nonpathogenic strains (harboring neither tdh gene nor trh gene) contained partial genes of VPaI-2, T6SS, and type I pilus. Genes of VPaI-4 were exclusively present in the pandemic strains. Genes of VPaI-3 were present in most of the pandemic strains and a small percentage of nonpathogenic strains, mainly O3:K6 strains. VPaI-6 and biofilm-associated genes were harbored by almost all the strains, irrespective of their pandemic, pathogenic, or nonpathogenic traits.