Abstract: To investigate the endophytic bacterial diversity in the three medicinal plant species Codonopsis pilosula, Ephedra sinica, and Lamiophlomis rotata in Ganzi of Sichuan, Southwest China, the total DNA of the three species were extracted by stringent surface sterilization, and studied with length heterogeneityPCR (LH-PCR) method. For the same plant species, their root, stem, and leaf LH-PCR profiles were in a high level of similarity, with little differences in band richness. However, there existed great differences in the LH-PCR profiles among different plant species. C. pilosula had the biggest band richness, followed by E. sinica, and L. rotata. In the three plant species, the endophytic bacteria with an approximately 474 bp DNA length were dominant. The endophytic bacterial diversity of the plants was negatively correlated with rhizosphere soil available phosphorus content, but positively correlated with rhizosphere soil pH. Elevation and rhizosphere soil total nitrogen content were the important environmental factors affecting the distribution of enophytic bacteria in these plant species. The information of population diversity obtained from LH-PCR could more intuitively reflect the differences of bacterial diversity among different plant species, and thus, LH-PCR would be available to be used for analyzing the endophytic bacterial diversity in medicinal plants, providing information and guidance for the further isolation of microbial resources.