Translucent post-larvae disease (TPD) is a new emerging disease-causing massive mortality in shrimp at the larval stage. A highly virulent strain of Vibrio parahaemolyticus is reported to be associated with TPD (VpTPD). Although few genomes from VpTPD strains isolated from China have been characterized, no comprehensive genomic studies have yet been carried out for VpTPD strains isolated from outside of China. This study characterized the whole genome sequence of Vibrio parahaemolyticus strain causing TPD (VpTPD). The whole-genome sequence of VpTPD was ~5.5 Mb, consisting of two chromosomes and three plasmids. One of the three plasmids encodes 3 (VHVP) proteins, causing TPD in shrimp. Genomic characterization revealed that VHVP is a Tc-like toxin complex. Laboratory bioassay conducted using VpTPD revealed that the bacterial isolate used in this study causes mortality at the late stage of post larvae (PL10-PL20). The findings broaden our understanding of the pathogenicity of the VpTPD strain and the diagnosis of TPD.