Cathepsins are lysosomal/cysteine proteases belong to papain family (C1 family) that is involved in intracellular protein degradation, antigen processing, hormone maturation, and immune responses. In this study, member of cathepsin family was identified from Manila clam (Mc-Cathepsin D) and investigated the immune response against brown ring disease (BRD) causing Vibrio tapetis challenge. The identified Mc-Cathepsin D gene encodes characteristic features typical for the cathepsin family including eukaryotic and viral aspartyl protease signature domain and two highly conserved active sites ($^{84}VVFDTGSSNLWV^{95}$ and $^{270}IADTGTSLLAG^{281}$). Moreover, MC-Cathepsin D shows higher identity values (-50-70%) and conserved amino acids with known cathepsin D members. Transcriptional results (by quantitative real-time RT-PCR) showed that Mc-Cathepsin D was expressed at higher levels in gills and hemocytes than mantle, adductor muscle, foot, and siphon. After the V. tapetis challenge under laboratory conditions, Mc-Cathepsin D mRNA was up-regulated in gills and hemocytes. Present study indicates that Mc-Cathepsin D is constitutively expressed in different tissues and potentially inducible when infecting BRD by V. tapetis. It is further suggesting that Mc-Cathepsin D may be involved in multiple role including immune response reactions against BRD.