Abstract: The denaturing gradient gel electrophoresis (DGGE) method was applied to investigate the diversity and community structures of the endophytic actinomycetes isolated from the different tissue parts of Medicago ruthenica grown in Ganzi, Sichuan Province. The result indicated that the diversity and community structures of the endophytic actinomycetes were significantly different among the plant tissue parts of root, stem, leaf and flower. The highest diversity index (H) and richness (S) were found in the plant flower, then, in the root, stem and leaf, respectively. The eveness (E_H) of the actinomycetes was higher in the leaf, than that in the root, stem and flower, respectively. The similarity of the community structures was significantly different among the plant tissue parts, except that between the leaf and stem. The results of DGGE bands sequencing showed that the majority of the clones were the genus Streptomyces, the rest of 43% clones were rare actinomycetes. In addition, the dominant band A23 and common band A12 also showed the clone of rare actinomycetes, which indicated that some rare actinomycetes were the dominant species in the medicinal plant M. ruthenica. All of the results in this work revealed the high diversity of endophytic actinomycetes in the plant tissues of M. ruthenica, and the richest was found in the flower. M. ruthenica in Ganzi should be a good plant resource for isolation of endophytic actinomycetes.