Vibrio parahaemolyticus is one of the most important pathogens capable of causing foodborne gastroenteritis in China, Japan, and other countries. Pathogenic V. parahaemolyticus has been known to produce either thermostable direct hemolysin (TDH), TDH-related hemolysin (TRH), or both. The emergence of a new clone in 1995, V. parahaemolyticus O3:K6, has resulted in the first documented pandemic spread of V. parahaemolyticus. In this study, 235 isolates from clinical and food sources were characterized by determining the presence of known virulence factors (tdh, trh), systematic genetic markers (toxRS/new, pandemic group-specific sequence [PGS], orf8) specific for V. parahaemolyticus O3:K6 clone and its clonal derivatives, three important genomic islands (GIs) (VPaI-1, VPaI-5, and VPaI-7), and two type III secretion systems (T3SS1 and T3SS2). Our results showed that all 235 isolates harbored all or part of the T3SS1 genes. All the 103 tdh-positive strains harbored all or part of the VPaI-7 and T3SS2 genes. A total of 91 isolates including six foodborne isolates belonged to a pandemic clone in which eight isolates lacked orf8. All pandemic strains harbored VPaI-1 and VPaI-5 except one O4:K68 strain that lacked VPaI-5 altogether. Twelve clinical pathogenic strains had VPaI-7 and T3SS2 but lacked VPaI-1 and VPaI-5. Thirteen nonpathogenic clinical strains and 119 foodborne strains, including six foodborne pathogenic trh-positive strains, only harbored T3SS1 genes. These results indicated that O3:K6 and its serovariants were the main pandemic clone in China. VPaI-1 and VPaI-5 genes were specifically correlated with pandemic strains while VPaI-7 and T3SS2 were closely associated with tdh-positive strains.