Abstract:The sequences of nrDNA internal transcribed spacers(ITS)(including 5.8S rDNA)of 9 species and 2 varieties in Sect.Sphenanthera,4 species in Sect.Begonia were examined and analyzed B.cirrosa (sect.Coelocentrum),B.henryi(Sect.Reichenheimia)as outgrorp.The length of these sequences is 648-743bp,and the aligned length of ITS region is 756 position,which provides 26.41% variable sites and 10.11%phylogenetical informative sites when gaps are treated as missing.Six most parsimonious trees,with length of 286,consistency index(CI)of 0.8287 and retention in dex(RI)of 0.7841 were obtained by PAUP 4.0b8 analysis.