Viruses are the most diverse biological entities ranging from simple forms with just a few genes to complex forms with hundreds of proteins. Among all viruses, RNA viruses are the most abundant, accounting for 70% of them. The diversity and role of RNA viruses in microbial ecosystems is poorly understood. The rhizospheric region enriched with microbial diversity provides an optimal environment to explore the functional interactions of RNA viruses with plants. With the advancement of high-throughput RNA sequencing techniques, it is now possible to explore the previously unexplored RNA virome in the rhizosphere. However, the bioinformatics pipeline for the taxonomical classification and functional annotation of RNA viruses using metatranscriptome data has not yet been well established. In this chapter, we describe the stepwise pipeline to explore the RNA virome through metatranscriptomic approach.