We investigated fecal microflora in the fecal samples of three species of Elaphe (E. carinata, E. schrenckii and E. anomala) which were fed in captivity in laboratory by using a V4﹣V5 region of 16S rRNA gene amplicon sequencing and analyzed the diversity and composition of the microflora. The results showed that the number of OUTs was 192 and the number of shared OTUs was 116 in all samples (Fig. 1). The diversity indexes (Shannon and Simpson) were significantly different between the E. carinata and the E. schrenckii, but the E. anomala had no significant difference when compared to the above two species. There was no significant difference in ace and chao1 among the three species (Table 1). Eight phyla were detected in the samples, but only three phyla, Firmicutes, Bacteroidetes and Proteobacteria were shared by these three species (Fig. 3). The ranking of relative abundance of the three phyla was obviously different. There were 4 genera (Bacteroides, norank_f_Porphyromonadaceae, Enterococcus, Escherichia-Shigella), and the average relative abundance was 77.92% in the E. carinata faeces, there were 9 genera (Bacteroides, Bacillus, Enterococcus, Clostridium_sensu_stricto_1, Clostridium_sensu_stricto_11, Paeniclostridium, Aeromonas, Escherichia-Shigella, Proteus, total of average relative abundance is 75.53%) in the E. schrenckii faeces. There were 6 genera (Bacteroides, norank_f_Porphyromonadaceae, Enterococcus, Clostridium_sensu_stricto_1, Edwardsiella, Escherichia-Shigella), and the average relative abundance was 67.42% in the E. anomala faeces (Table 2). Notably, Escherichia-Shigella had the highest relative abundance in E. carinata faeces; Clostridium_sensu_stricto_11 had the highest relative abundance in E. schrenckii faeces; Bacteroides had the highest relative abundance in E. anomala faeces. There is significant difference in the composition of microbial communities in the faeces among the three species. Under the same feeding environment and food condition, the main factors determining the difference of the microbial communities may be closely related to the specific genomes of each species, which needs further clarification.