In order to detect the codon usage variation of different genomes, the begomoviruses were divided into three groups including the Old World begomoviruses with monopartite genomes (OM), the Old World begomoviruses with bipartite genomes (OB), and the New World begomoviruses with bipartite genomes (NB). The distribution of the three groups along the first two major axes showed that the Old World monopartite begomoviruses and the New World bipartite ones were located in two independent fields, indicating that the two groups of begomoviruses exhibit a different codon usage pattern. Because the species with a close genetic relationship always present a similar codon usage pattern (Sharp et al., 1988) , the genetic relationship of the two groups of begomoviruses should be far removed from each other. As to the Old World begomoviruses with bipartite genomes, we found that the majority of them exhibited a similar codon usage pattern with the Old World monopartite begomoviruses, and a few of them showed a similar codon usage to the New World bipartite begomoviruses. An explication of this result might be that a number of Old World bipartite begomoviruses evolved to adopt the codon usage pattern of some Old World monopartite begomoviruses.