Lysozymes are the important enzyme factor of the innate immune system to protect from bacterial infections. In this study, an ortholog of chicken-type lysozyme (AcLysC) from the yellowtail clownfish (Amphiprion clarkii) was identified and characterized structurally and functionally. The full-length cDNA sequence (595 bp) of AcLysC is comprised of an open reading frame made up of 429 bp, encoding a polypeptide of 127 amino acid (aa) with a predicted molecular mass of 14.2kDa. In silico analysis of AcLysC revealed the presence of signal peptide at 1-17 aa and there are two catalytic residues (Glu50, Asp67) and three Ca2+ binding sites (Thr98, Leu103, Ala104). Homology studies indicated that AcLysC showed the highest sequence identity (98%) with of Amphiprion ocellaris. In healthy clownfish, AcLysC mRNA showed a constitutive expression in all the tissues examined, with the highest expression in liver and the least expression in blood. In response to the immune challenges lipopolysaccharide (LPS), Vibrio harveyi, and poly I:C injection, the expression of AcLysC was significantly upregulated. The recombinant protein of AcLysC was produced by cloning in to pMAL-c5X vector and purified using maltose affinity chromatography method. In protein assay, lytic activities of AcLysC were highly active at pH 3.0 to 4.0. These results provide evidences for the vital immunological role and bacteriolytic potential of AcLysC for the protection of yellowtail clownfish.