Abstract: We investigated the endophytic diversity,the factors affecting isolation and cultivation of endophytes in Juglans regia and Toddalia asiatica,such as seasons,areas,age of trees and sampling sites.In the end of Spring and the beginning of Summer,it was easier to obtain more species of endophytes when the hosts with an old tree-age.The five different disinfectants were tested with different concentrations and time,and the optimum condition of the isolation and cultivation of endophytes were screened out in the present study.It was showed that the approaches disinfecting samples got good effect,with 3.0% H2O2 for 30—120 s,0.5% KMnO4 for 30—120 s,75% ethanol for 60—120 s and 4% bleaching powder for 30—120 s.This attempt was also to provide the basic data for the further development and utilization of endophytes in medicinal plant.