Abstract: In order to control the gray mold effectively,the distribution,physical and chemical properties,and tertiary structure of pectinase in Botrytis cinerea genome were analyzed by bioinformatics in this study.The results showed that there were 6 PG,4 PME and 4 PEL in B.cinereagenome.PG sequences were 370-514 aa in length with 16-21 aa signal peptides and abundant phosphorylation sites.PME sequences were 327-348 aa in length with 18-23 aa signal peptides and many phosphorylation sites,but no N-glycation sites.While PEL protein sequences were 236-353 aa in length,with 17-20 aa signal peptides,and abundant in O-glycations sites and phosphorylation sites.Conservative regions existed three kinds of pectinase amino acid sequence respectively.Tertiary structure prediction results showed that similar domain structure presented in the same family.Evolutionary analysis indicated that pectinases were conserved in B.cinereagenome.