The present experiment was conducted to investigate the expression of innate immune-related genes TLR9, type I IFN and Mx3 in tissues of kidney and spleen in juvenile koi (Cyprinus carpio L) after induction with bacterial DNA (bDNA) stimulation, koi ranavirus (KIRV) infection, and combined administration bDNA followed by the virus. The study revealed that the mRNA expression of TLR9 was continuously upregulated in kidney between 24 h (35 fold) to 96 h (126 fold) in bDNA pretreated fish infected with KIRV. TLR9 was upregulated in spleen from 1.1 fold (24 h) to 19 fold (96 h) when stimulated with bDNA to 4.11 fold (96 h) upon virus administration. Type I IFN gene was upregulated in spleen of koi at 24 h (50 fold) and decreased later till 96 h (1.08 fold) during virus infection. The expression of IFN in both kidney and spleen was down regulated from 24 h to 96 h post infection in both fish treated with bDNA and virus infected fish pre-treated with bDNA. Infection with KIRV induced high Mx3 expression at 24 h in kidney in all three treatments, while it showed increasing trend in spleen with high expression at 96 h especially in virus infected fish pretreated with bDNA. These studies revealed that the mRNA expression profiles of immune-related genes in koi were stimulated by bDNA and KIRV. The study also revealed the immune-stimulatory potency of bDNA to enhance innate immune response similar to CpG ODNs that could be used as adjuvant preparation in viral vaccines for fish.