The current study aimed to identify cytochrome c oxidase subunit 1 (ONCOX1) in Tilapia (Oreochromis niloticus) immunized by formalin-killed Flavobacterium columnarae. Suppressive subtractive hybridization (SSH) was utilized to construct a cDNA library and semi-quantitative RT-PCR analysis used to examine Oreochromis niloticus cytochrome c oxidase subunit 1 (COX1) gene expression. COX1 cDNA is composed of 1139 bps with a 1107 bps open reading frame, the predicted gene product is 369 amino acids with molecular weight of 40.16 kDa. The amino acid sequence revealed high identity with subunit 1 from Oreochromis mossambicus. Compared to ß-actin, the semi-quantitative RT-PCR revealed that ONCOX1 expressed in tissues of stimulated fish as up-regulated gene suggesting that this member of COX genes is probably involved in the general immune response against the pathogenic bacteria.