Vibrio harveyi is a common sort of pathogenic bacterium in marine, which annually gives rise to huge financial losses in aquaculture industry. Flagellin is one of the important virulence factors for bacteria, but meanwhile it is also a preferable vaccine candidate. In this study, we have identified and analyzed two flagellin antigens of V. harveyi, FlaB and FlaC; and moreover, on this basis, two subunit vaccines (rFlaB and rFlaC) were constructed, and the potential as vaccines against V. harveyi infection were determined and compared. Sequence analysis indicated that the coding region of FlaB was 1131 bp, sharing the highest sequence identity (97.07 %) with the counterparts of V. campbellii, and that FlaC (1155 bp) shared the highest sequence identity (98.18 %) with the counterparts of V. campbellii. The vaccine potential of subunit vaccines, rFlaB and rFlaC, were analyzed in the Epinephelus coioides model. The results showed that fish vaccinated with rFlaB or rFlaC at 4-week post- vaccination (p.v.), exhibiting a relative percent survival (RPS) of 81.8 % and 59.1 %, respectively; when fish were vaccinated with rFlaB or rFlaC at 8-week p.v., the RPS of rFlaB and rFlaC were 76.2 % and 42.9 %, respectively. Compared to control group, immunological analysis showed that both rFlaB and rFlaC could elicited specific antibody expression and innate immune responses. Of note, rFlaB could induce higher levels of IgM, AKP, LZM, ACP and SOD activity in fish in comparison with rFlaC. Additionally, qPCR results manifested that the expressions of IL-1 beta, CD4, CD8 alpha, IgM, IFN gamma, MHCI alpha, MHCII alpha, TLR5M and TLR5S were significantly up-regulated in the fish immunized with rFlaB and rFlaC, indicating their ability to activate innate immunity and trigger the inflammatory and cell immune responses. Overall, FlaB is superior to FlaC as regards potential as vaccines. This research has developed two promising subunit vaccines against diseases caused by V . harveyi that are well-suited for application in aquaculture.