The variability of cacao swollen shoot virus (CSSV) was studied in two areas of Togo with distinct epidemiological backgrounds, Kloto and Litime´. This molecular study was based on 120 sequence comparisons of the first part of ORF3 of the viral genome. The phylogenetic study distinguished three groups of CSSV isolates, A, B, and C, with clear geographical differentiation between the Kloto and Litime´ areas. The only group detected in Kloto was group C, whereas the Litime´ area only contained isolates from groups A and B, which most probably originated from Ghana. The divergence between the three groups strongly suggests a different origin for each of the groups.