[Objective] The composition and diversity of intestinal microbial diversity of Chinese giant salamander (Andrias davidianus) were investigated. [Methods] The composition and diversity of intestinal microbial diversity of Chinese giant salamander were analyzed by culture-independent method. The total DNA were extracted by Fecal DNA Isolation Kit of Mo Bio company. The 16S rRNA gene of intestinal microbial diversity of Chinese giant salamander were amplified by universal PCR primers. Positive clones were analyzed by PCR restriction fragment length polymorphism (PCR-RFLP) and the clones with unique Hae Ⅲ patterns were selected for sequencing and constructing 16S rRNA gene phylogenetic tree. [Results] A total of 101 positive clones that randomly screened from the library were fall into 28 operational taxonomic units (OTUs) based on the result of Hae Ⅲ digestion and sequencing. These clone squences were divided into 4 phyla with phylogenetic analysis, which consisted of the Proteobacteria, Clostridia, Bacilli and Chlamydiae, of which Proteobacteria accounting for 92.08% 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 OTU on phylogenetic tree is independent and failed to determine its classification. [Conclusion] The intestinal microbial diversity of Chinese giant salamander harbors a diversity endophytic bacterial and maybe existence new OTUs.