Twelve strains of pathogenic Vibrio parahaemolyticus isolated from Litopenaeus vannamei with acute hepatopancreatic necrosis disease (AHPND) were chosen, and their genetic characteristics were analyzed by the multilocus sequence typing method. Seven house-keeping genes (dnaE, gyrB, recA, dtdS, pntA, pyrC and tnaA) of V. parahaemolyticus were selected as target genes for PCR amplification and nucleic acid sequencing. The sequences of AHPND-causing V. parahaemolyticus in this study were uploaded to the PubMLST database for multi-alignment to determine the sequence type of each strain. MLST data of AHPND-causing V. parahaemolyticus from other areas were collected and the genetic evolution was analyzed by MEGA 5.0 and eBURST V3 software. AHPND-causing V. parahaemolyticus isolated from Guangdong province in 2014 belonged to the new sequence type ST1710(42, 134, 99, 79, 141, 41, 51). Compared with other sequence types in PubMLST database, it has the high homology with ST415 and ST975. The 9 STs of AHPND-causing V. parahaemolyticus were separated by eBURST into two doublets and five singletons. Phylogenetic tree analysis showed that the new sequence type ST1710 was similar to the singletons ST975. Our study is the first report of molecular epidemiology of AHPND-causing V. parahaemolyticus strains in China using multilocus sequence typing, and enriches the PubMLST database and provides an insight into their evolutionary mechanisms.