Abstract: Ten DNA regions were sequenced for gene sequencing study on Handeliodendron bodinieri.These ten DNA regions were chloroplast DNA included rpl32-trnL,trnH-psbA,trnL-F,trnS-G,trnT-L,matK,trnH-trnK and rps16,nrDNA ITS(nuclear ribosomal DNA internal transcribed spacer)included ITS1-4 and ITS5f-2r.By sequence alignment,it showed 10 fragments of 96 individual gene sequences were almost identical.Genetic distance ranged from 0.000~0.001.Horse Aesculus chinensis Bunge was selected as outside groups,96 individuals on the same branch,little bits of information.So,the genetic sequencing method was difficult to apply by using the method of cpDNA and nrITS gene sequencing to divide the Handeliodendron bodinieri clusters.