[Objective] We investigated the composition and diversity of endophytic bacterial in Taxus chinensis. [Methods] The composition and diversity of endophytic bacterial in Taxus chinensis were analyzed by culture-independent method. When total community DNA were extracted, a pair of bacterial PCR primers were used for endophytic bacterial 16S rDNA gene amplification and a clone library was constructed for the Taxus chinensis DNA samples. Positive clones were analyzed by PCR restriction fragment length polymorphism (PCR-RFLP) and the clones with unique patterns were selected for sequencing and constructing 16S rRNA gene phylogenetic tree. [Results] Based on Hae Ⅲ digestion and sequencing result, a total of 158 positive clones that randomly screened from the library were fall into 26 operational taxonomic units (OTUs). These clone squences were divided into 4 phyla with phylogenetic analysis, which consisted of Alpha, Beta, Gamma and delta subclasses of the Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes, of which Proteobacteria accounting for 58.86% of the total number of clones was the absolutely dominant group. Sequence alignment showed these clone sequences have high similarities with 20 genus that had been reported. In addition, one OUTs on phylogenetic tree is independent and failed to determine its classification. [Conclusion] Taxus chinensis harbors a diversity endophytic bacterial and maybe existence new taxon.