RNA-dependent RNA polymerase (RdRp), B2 and capsid genes of Macrobrachium rosenbergii nodavirus (MrNV) of Indian isolate were polymerase chain reaction amplified, cloned and sequenced. Expression of the MrNV fusion recombinant proteins of RdRp (44.5 kDa), B2 (32.2 kDa) and capsid (58.4 kDa) was confirmed by Western blot analysis using anti-His mouse monoclonal antibodies. Polyclonal antibodies specific to purified recombinant MrNV capsid protein showed specificity against the capsid protein by Western blot. The protein sequence analysis of the partial RdRp gene of MrNV revealed the signature sequence along with the conserved core residues of the catalytic domain and indicated the presence of active sites, metal ion-binding site and nucleic acid-binding site residues. The Indian isolate of MrNV showed high RdRp and capsid gene sequence homology with the other MrNV geographical isolates. However, the Belize isolate was found to be the most distinct among the different geographical prawn nodavirus isolates due to the host specificity. Secondary structure prediction analysis of the MrNV capsid predicted it to be a DNA-binding protein consisting of α helix (22.91%), extended strand (24.80%), β turn (5.39%) and random coil (46.90%) regions.