Akirins are conserved nuclear resident NF-κB signaling pathway molecules. Isoforms of akirins found in various organisms are known to play diverse roles. In this study, we have characterized two akirin2 homologues from rock bream, OfAk2(1) and OfAk2(2). The proteins derived from OfAk2(1) and OfAk2(2) revealed the presence of nuclear localization signal. Multiple sequence alignment and pairwise alignment of OfAk2(1) and OfAk2(2) with the akirin homologues, revealed high conservation and identity. Phylogenetic tree analysis revealed that the distinct position of OfAk2(1) and OfAk2(2) was close to the fish homologues and separated from the mammals and invertebrates. Genomic structure characterization revealed two distinct structures. OfAk2(1) possessed 6 exons interrupted by 5 introns whereas OfAk2(2) possessed 5 exons interrupted by 4 introns. The promoter analysis revealed the presence of significant transcription factors, which suggests its regulation by diverse stimuli. In addition, transcript expression analysis using real time quantitative reverse-transcriptase polymerase chain reaction post immune challenges with lipopolysaccharide, Edwardsiella tarda and poly I:C revealed upregulation of both OfAk2(1) and OfAk2(2) in liver, spleen and head kidney.