In this study, Vibrio harveyi strain HY99 was isolated from a diseased Epinephelus coioides. A full-length HrpQ gene of the bacteria was cloned and the amino acid sequence analyzed. The length of HrpQ gene sequence was 1,302 bp and coded 433 Amino acids. HrpQ relative molecular weight of theoretical prediction and isoelectric point were 48.002 kDa and 5.08 respectively. This protein was hydrophilic and there was one transmembrane region. There were three N-glycosylation sites. Structural analysis showed that the protein belonged to the FHA, Yop-YscD ppl superfamily. Secondary structure was composed of 31.41% α-helices, 21.71% extension chains, 7.16% beta turns and 39.72% random curls. The 3D structure of HrpQ protein was predicted to be a monomer similar to the 3D structure of the YscD putative type III secretion protein confirming that HrpQ is a T3SS protein and can be activated in vivo. This study provides a theoretical basis for further study on the function of HrpQ protein.