Sequence analysis and structure prediction of violaxanthin de epoxidases(VDE) were performed, based on the knowledge of bioinformatics, with the biological databases(GenBank,Swiss Prot and Prosite) and tools(PHDsec and SignalP) supported by Internet, and software(DNAstar).The characteristics of transit peptides, conserved sites, motifs, and secondary structure of VDEs were obtained, meanwhile, their functions were analysed.