The variation analysis of the base composition for begomovirus genes showed that AV1 and BV1 genes exhibit a stronger codon usage bias and a higher gene expression level. Thus CAI values of different gene samples were calculated using the AV1 gene as a reference set. The results of correlation analysis indicated the reliability of choosing AV1 gene as a high expression gene sample for begomoviruses. Then 14 codons were determined as the major optimal codons for begomoviruses. That will be very important during the design of degenerate primers, the introduction of point mutation, the modification of the virus genes and the investigation of the evolution mechanism of species at the molecule level.