A new disease similar to whitish tail disease (WTD) was observed in larvae and post-larvae of Macrobrachium rosenbergii in hatcheries and nursery ponds located at Nellore, Vijayawada and Chennai, India. Reverse transcriptase polymerase chain reaction (RT-PCR) assay on these samples revealed the presence of Macrobrachium rosenbergii nodavirus (MrNV) and extra small virus (XSV) in infected larvae and post-larvae, as reported in China. Published primers and self-designed primers specific for MrNV were tested and compared for sensitivity with MrNV samples collected in India. Our designed primer sets 4 and 2 gave amplicons of 425 and 590 bp, respectively, with improved sensitivity to the level of 0.25 fg of total RNA when compared to 25 fg of total RNA for the previously published method. XSV detection was based on a recently published RT-PCR protocol. This is the first report on the occurrence of MrNV and XSV in WTD of freshwater prawn from India.