Synonymous codon usage variation had been investigated in protein-coding genes of geminiviruses.Most of the genes were speculated to be lowly expressed,but coat protein (CP) gene was considered as relatively highly expressed one,which preferred to use those codons ending with A or T.The codon usage variation in geminiviruses was influenced by several factors such as mutation bias and translational selection.The codon usage patterns in geminiviruses were gene-specific and certain host-specific.Cluster analysis based on relatively synonymous codon usage (RSCU) could efficiently and effectively reflect the difference between the monocot-infecting and dicot-infecting geminiviruses,and to a certain extent reflect the evolutionary relationship among them.