Next-generation sequencing (NGS) technologies are continuously being developed and are becoming a more cost-effective tool for the characterization of viral genomes. Whole genome sequencing of segmented viruses, such as epizootic hemorrhagic disease virus (EHDV), provides insights into the molecular epidemiology as well as such viral evolutionary mechanisms as genetic reassortment. Here, we present a detailed method for obtaining full genome sequence data for EHDV using Illumina technology. The protocol includes details from RNA extraction and purification, the synthesis of cDNA, sequencing library preparation, to genome assembly.