The immune responses and protection efficacy of a vaccine containing inactivated formalin-killed Photobacterium damselae subsp. piscicida formulated with alum and different unmethylated Cytosine phosphorothioate Guanine oligodeoxynucleotides (CpG-ODN, including 2006, 2395, 1668, and control ODN 2137) as the adjuvant were investigated in cobia Rachycentron canadum. Results showed that, formulation with CpG-ODN 1668 significantly (P < .05) increased the expression of rctlr9a (11 and 20 fold in spleen and liver, respectively) and il-1β (4 fold in liver) in immunized fish. The highest lysozyme and peroxidase activities were also observed in fish immunized with CpG-ODN 1668 formulation. In addition, compared to other treatments, bactericidal activity using the bacterial survival percentage was significantly less in CpG-ODN 1668 formulation (25%). The antibody titer was significantly higher at 6 and 21 dpi from CpG-ODN 1668 (OD = 0.27 ± 0.02) and CpG-ODN 2006 (OD = 0.24 ± 0.018) formulations. Fish immunized with CpG-ODN 1668 and 2395 formulations protected R. canadum with survival rate of 90 & 70% by P. damselae subsp. piscicida until 3 weeks post-challenge. This study has indicated that different tlr9 agonists have different abilities to augment immune response and protection against Photobacterium. CpG-ODN 1668 can be used as an adjuvant for R. canadum vaccination.