To understand the evolutionary relationships among Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV), this study determined 64 nucleotide sequences from the variable P1 gene from major cassava producing areas of east and central-southern Africa. An amplicon of the P1 region of 31 isolates from Malawi and Tanzania as well as 33 previously reported sequences of virus isolates from Uganda, Kenya, Tanzania, Malawi and Mozambique were sequenced. Phylogenetic analyses revealed three major P1 clades of CBSVs including an intermediate clade of CBSV isolates, CBSV-Tanzania. Grouping of P1 gene sequences were indicated for distinct sub-populations of CBSV, but not UCBSV. Representatives of all three clades were found in both Tanzania and Malawi.