Ninety-four GB virus C/hepatitis G virus (GBV-C/HGV) RNA-positive serum samples were obtained from all over the world. We found that all 15 GBV- C/HGV isolates from the Pygmies and the Bantu in the Central African region had a 12-amino acid indel (i.e. insertion or deletion) in the non-structural protein (NS) 5A region. Phylogenetic analyses of the NS5A region, using GBV- A as an outgroup, showed that these 15 isolates had diverged from the common ancestor much earlier than the remaining isolates, indicating an African origin of GBVC/HGV.