To understand the basic mechanism of RNAi-mediated resistance in rice, we characterized the virus-derived small RNAs and miRNAs by Deep Sequencing (Zarreen et al. 2018). We found a predominant production of 21 nt/ 22nt (nucleotide) siRNA from RTBV in a continuous, overlapping and asymmetrical manner while there was negligible siRNA from RTSV. In addition, we found around 54 known miRNA in rice to be differentially regulated upon Tungro infection regulating the components of many important physiological and biochemical pathways. This was the first study of sRNA profile of tungro virus complex from infected rice plants.