White tail disease (WTD) is found to cause immense economic losses in hatcheries and farms, with mortalities often reaching 100% within 2 or 3 days. The pathogenic agents have been identified as Macrobrachium rosenbergii nodavirus (MrNV) associated with extra small virus (XSV), which are 27 and 15 nm in diameter, respectively. Experiments were carried out to characterize an Indian isolate of XSV capsid protein of 17 kDa (CP-17). The gene encoding CP-17 was cloned and its sequence analysed with sequences of other isolates such as French, Chinese, Taiwanese and Thai available in the GenBank using Bioinformatics tools such as BLASTn, clustal W and phylogenetic analysis. When compared with other isolates, 18-point mutations were observed in Indian isolate (XSV-IN) with few changes in amino acid residues. Homology comparison showed 99-96% identity with other isolates. Phylogenetic analysis revealed that the Indian isolate was closely related to Taiwanese and Chinese isolates than French and Thai. This shows that the possible origin of the disease in India was from Taiwan and China through the import of prawn seed decades ago.