Two species of Chinese medicinal plants, Salvia miltiorrhiza Bge. and Polygonatum sibiricum Red., were collected from Suining region of Sichuan province. The plants were disinfected with 0.87% hypoclorite under different time and treated with the methods of organic law and homogenate law, respectively. Then endophytes were isolated in the media HV, G2, S amended with which use different concentrations of potassium dichromate plus malidixic acid as inhibitors. The method of isolating endophytic actinomycetes from the medicinal plants was optimized. Fifty-two endophytic actinomycetes with different colony size, shape and color were isolated and purified. Twelve representative strains were chosen for genetic diversity study by 16S rRNA PCR-PFLP. Five clusters were abtained based the 16S rRNA PCR-RFLP pattens which indicated the high genetic diversity of the endophytic actinomycetes in medicinal plants.