It was speculated that monopartite begomoviruses emerged approximately 130 million years ago (Rybicki, 1994; Mansoor et al., 2006) , suggesting that the begomoviruses should have evolved from the original monopartite viruses. Rybicki (1994) suggested that the significant expansion of the New World begomoviruses might have occurred after the transmission of the Old World begomoviruses to those of the New World by whiteflies. Based on codon usage pattern analysis, it could be inferred that there was no direct relationship between the Old World monopartite begomoviruses and the New World bipartite ones. Interestingly, a small number of the Old World bipartite begomoviruses exhibited a similar codon usage pattern to the New World bipartite ones, which suggested that the ancestor of begomoviruses could have evolved from monopartite to bipartite ones before they were transferred to the New World areas. Subsequently it was not the Old World monopartite begomoviruses but the Old World bipartite ones that transmitted to the New World in a certain way and finally evolved into the New World bipartite begomoviruses. In other words, the New World bipartite begomoviruses probably resulted directly from the Old World bipartite ones, while the latter evolved from the Old World monopartite begomoviruses.