Using whole genome sequences from NGS data, this study produced the first coalescent-based species tree estimate for Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). This species framework led to the finding that CBSV has a faster rate of evolution when compared with UCBSV.  Furthermore, it was discovered that in CBSV, nonsynonymous substitutions are more predominant than synonymous substitution and occur across the entire genome. All comparative analyses between CBSV and UCBSV presented here suggest that CBSV may be outsmarting the cassava immune system, thus making it more devastating and harder to control.