Hepcidin, a cysteine-rich antimicrobial peptide, is an important effector molecule in the innate immune system. Recently, Brachymystax lenok has become to be a valuable cold-water fish in China, particularly as the wild resources are rapidly declining. In this study, the hepcidin gene of Brachymystax lenok (Blhepc) has been cloned. The 870-bp mRNA contains a coding sequence (CDS) of 267 bp that encodes 88 amino acid residues. Amino acid sequence identities of Blhepc with hepcidin in Oncorhynchus mykiss, Salmo salar, and Hucho taimen were found to be 93.18%, 89.77% and 93.18%, respectively. Phylogenetic analysis indicated that Blhepc was clustered in the family Salmonidae. The putative signal peptide and the mature peptide contained 24 and 25 amino acid residues, respectively. The RXXR motif for recruitment of propeptide convertase was identified upstream of the mature peptide of Blhepc by sequence analysis. The N-terminal amino acid residues of the mature Blhepc peptide were Q-S-H-L, a structure involved in regulating iron metabolism. Eight conserved cysteine residues in the mature peptide were held together by four disulfide bonds. Expression profiling of Blhepc indicated its highest level in the liver; its expression was stronger in males than in similar-aged females. Moreover, its expression in the liver increased significantly with age. Expression of Blhepc in six immune tissues showed increase in various degrees when challenged with Aeromonas salmonicida and Aeromonas hydrophila. A synthetic Blhepc mature peptide was validated to have significant antimicrobial activity against gram-negative and gram-positive bacteria and fungi in vitro. These results show that Blhepc may be an important component in the innate immunity of Brachymystax lenok, which could provide antimicrobial activities against invading pathogens.