In order to screening podophyllotoxin biosynthesis related differentially express genes among podophyllin plant species,we constructed a suppression subtractive hybridization(SSH) library from root and rhizome of Dysosma tsayuensis Ying and Sinopodophyllum hexandrum (Royle) Ying.201 positive clones randomly picked from the SSH library were sequenced,and then 183 qualified sequence ESTs which represent 17 unique ESTs through preprocessing,assembling,clustering,annotation and functional classification from Dysosma tsayuensis were obtained.Among them,12 unique ESTs which annotated with database were further classified into functional groups including photosynthesis ,biosynthetic metabolism,transcriptional regulation,etc,accouted for 70.6%.5 unique ESTs were nonannotated or did not match any entry in the databases,accouted for 29.4%.These results showed that we successfully constructed a SSH library of Dysosma tsayuensis Ying and Sinopodophyllum hexandrum (Royle) Ying,which provided a foundation for revealing the podophyllotoxin biosynthetic pathway and its regulation mechanism.