This research uncovered twelve new whole genomes, including seven of Cassava brown streak virus and five of Ugandan cassava brown streak virus. This doubles the genomic sequences available in the public domain for these viruses. These new sequences disprove the assumption that the viruses are limited by agro-ecological zones, show that current diagnostic primers are insufficient to provide confident diagnosis of these viruses and give rise to the possibility that there may be as many as four distinct species of virus. Using NGS sequencing technologies and proper phylogenetic practices will rapidly increase the likelihood of finding the solution to sustainable cassava production.