[Objective] The ability of accumulation of Zn and Cd between the hyperaccumlating and non-hyperaccumulating ecotypes of Sedum alfredii differed significantly, which might be related to their endophytic bacteria communities. Thus, the objective of this study is to investigate and compare the endophytic bacterial communities between two ecotypes of S. alfredii. [Methods] By using high-throughput sequencing technique, a research on the diversity of endophytic bacterial communities in leaves and stems samples of the hyperaccumulating and non-hyperaccumulating of S. alfredii was conducted. The samples of the hyperaccumulating of S. alfredii were collected from an old lead-zinc mine located in Quzhou city, the west of Zhejiang province, and the non-hyperaccumulating of S. alfredii were collected from a tea garden located in Jiuxi, Hangzhou city, the north of Zhejiang province. [Results] A total of 366 783 sequences and 39 948 operational taxonomic units (OTUs) were obtained from the four samples (at the level of 97%). The index of Shannon indicated that endophytic bacterial biodiversity in the leaves of two ecotype of S. alfredii were consistenly higher than in the stems, endophytic bacterial biodiversity in the leaves of hyperaccumulator ecotype of S. alfredii were higher than in the leaves of non-hyperaccumulator ecotype of S. alfredii, while the reverse was true for the stem samples. Endophytes in the leaves and stems samples of the hyperaccumulator ecotype of S. alfredii included 26 and 21 phyla, 123 and 117 families respectively, while the non-hyperaccumulator ecotype of S. alfredii included 43 and 22 phyla, 175 and 83 families respectively. In addition, the most abundance associated with the four sample libraries were consistently found to be related to Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Cyanobacteria. On the genus level, the most abundance bacteria associated with the leaves and stems of hyperaccumulator ecotype of S. alfredii were Synechococcus and Plesiomonas, while Pseudomonas and Dechloromonas were for the leaves and stems of non-hyperaccumulator ecotype of S. alfredii. [Conclusion] Diverse communities endophytes inhabit leave and stems of the two ecotype of S. alfredii, while the most endophytes diversity of the four samples was the leave of hyperaccumulator ecotype of S. alfredii.