Begomoviruses are single-stranded DNA viruses and cause severe diseases in major crop plants worldwide. Based on current gcnomc sequcncc analyses, we found that synonymous codon usagc variations in the protein-coding genes of begomoviruses arc mainly influenced by mutation bias. Base composition analysis suggested that the codon usage bias of AV1 and BV1 genes is significant and their expressions are high. Fourteen codons were determined as translational optimal ones according to the comparison of codon usage pattcms bctwccn highly and lowly expressed genes. Interestingly the codon usagcs bctwccn bego moviruses from thc Old and the New Worlds are apparently different, which supports the idea that the bipartite bcgomoviruses of the New World might originate from bipartite ones of the Old World, whereas the latter evolve from the Old World monopartite begomoviruses.