Red-body disease is one of the most severe diseases of Litopenaeus vannamei. An outbreak of Litopenaeus vannamei red-body disease happened in a large-scale breeding farm in Zhejiang Province, 2011, with the mortality rate of >90%. A total of ten bacterial isolates were collected from the hepatopancreas of diseased shrimps, which were responsible for this outbreak. These isolates were identified as Vibrio parahaemolyticus by Vitek and 16S rRNA sequence analysis. Multilocus sequence typing (MLST) based on the concatenated genes dnaE-gyrB-recA-dtdS-pntA-pyrC-tnaA demonstrated that these isolates belonged to three novel sequence types (ST), with one isolate to ST413, seven to ST414 and two to ST415. ST413 contained two novel allelic profiles, recA-166 and tnaA-121, and ST414 harbored one novel allelic profile, gyrB-219. These novel allelic profiles and STs had been confirmed and deposited by the MLST website (http://pubmlst.org/vparahaemolyticus/). MLST results indicated these V. parahaemolyticus isolates did not originate from the same clone and exhibited remarkable genetic diversity. On the other hand, all of these isolates contained molecular markers for pandemic group, including a unique sequence within the toxRS operon, encoding transmembrane proteins involved in the regulation of virulence-associated genes, and VPA1168 within an 16-kb insertion, which encodes a hypothetical protein with approximately 80% similarity to the Mn2 and Fe2 transporter in Vibrio vulnificus. Also these isolates had the same virulence-associated gene composition (tlh tdh-trh-T3SS1 T3SS2-) and antimicrobial sensitivity profiling. Absence of tdh and trh, which had traditionally been thought to be critical for the virulence of V. parahaemolyticus, did not lead to the reduction of bacterial pathogenicity in Litopenaeus vannamei. Overall, these V. parahaemolyticus isolates might represent distinct variants within PG.