In this study, we have reported a full length cDNA of cathepsin B identified from the constructed cDNA library of snakehead murrel Channa striatus by genome sequence FLX technology.The identified full length C. striatus cathepsin B (CsCath B) is 1486 base pairs (bp) long which contains 990 bp open reading frame (ORF).The ORF region encodes 330 amino acids with a molecular mass of 36 k Da.This amino acid sequence contains three thiol protease motifs at 101-112, 275-285 and 292-311 with their respective active sites viz., Cys 107 , His 277 and Asp 297 .CsCath B exhibited the maximum similarity (87%) with Cath B from mangrove red snapper, Lutjanus argentimaculatus.Phylogenetically, CsCath B is clustered together with the fish groups belonging to perciformes.A predicted 3D model of CsCath B revealed 11 α-helix and 10 β-strands.CsCath B contains higher percentage (10%) of coils due to the presence of many glycine residues (36 residues).The highest gene expression (P<0.05) was noticed in liver.Further, the expression was induced with fungal (Aphanomyces invadans) and bacterial (Aeromonas hydrophila) infections.The predicted antimicrobial region of CsCath B was synthesized to study its antimicrobial property.The peptide exhibited the antimicrobial activity towards Gram negative and Gram positive bacteria.The overall results indicate that CsCath B is a potential molecule for further studies on murrel defense mechanism.