Abstract: Portunus trituberculatus is an economically important aquaculture species in China. As crustacean, it is lack of adaptive immunity and can induce effective immune responses to resist pathogen relying on innate immunity. Vibrio parahemolyticus and white spot syndrome virus (WSSV) have caused significant economic damage to P. trituberculatus aquaculture. High mobility group box (HMGB) proteins are known to be involved in diverse functions in mammalian cells. In crustacean, very limited studies on HMGB proteins have been documented. To investigate the role of high mobility group box (HMGB) proteins in innate immune system of P. trituberculatus, the HMGB homologue cDNA from P. trituberculatus (named PtHMGBa) was first cloned by using the technology of rapid amplification of cDNA ends (RACE) in our study. The full-length cDNA of PtHMGBa was 1030 bp in length, which includes an open reading frame (ORF) of 681 bp, a 255 bp 3′ untranslated region and a 94 bp 5′ untranslated region. The ORF encoded a polypeptide of 227 amino acids with a predicted molecular weight of 25.82 kD. The polypeptide contained two HMG boxes domain and a C-terminal acidic tail composed of 24 rich Asp/Glu residues. The BLAST analysis showed that HMGB shared the highest homology with Litopenaeus vannamei HMCBa. The expression of PtHMGBa was mainly distributed in the haemocytes and hepatopancreas. A weak expression was detected in the eyestalk. Quantitative Real-time PCR analysis showed that PtHMGBa transcripts up-regulated significantly in haemocytes at 6h post V. Parahemolyticus inflection and up-regulated significantly in hepatopancreas at 48h post infection. Meanwhile, PtHMGBa transcripts significantly up-regulated in haemocytes at 12h post WSSV inflection, and the same result was observed in hepatopancreas. Our results suggested that PtHMGBa may play important roles in innate immunity of the crab, and would provide useful information for the research of immune regulation in P. trituberculatus and other crustaceans.