Because of their destructive effect on cash crops (Moffat, 1999; Moriones and Navas-Castillo, 2000; Mansoor et al., 2006) , numerous studies on begomoviruses have been conducted to understand their symptoms, host range, distribution, genome structure, gene function, and so on Zhou et al., 2003) . In this paper, we report the analysis of codon usage bias in begomoviruses and also perform an evolutionary analysis based on their codon usage pattern.