Objective To investigate the characteristics of gut microbiota in SD rat model of diabetes mellitus induced by streptozotocin (STZ). Methods Twenty?five male SD rats were randomly divided into control (C) (n =10) and diabetes (M) (n =15) groups. Rats in the group M received intravenous injection of streptozotocin (30 mg/ kg) once per day for 5 consecutive days. Fecal samples were collected and examined for the V3 region of the 16S rDNA gene by Illumina Miseq high?throughput sequencing. The abundance and composition of gut microbiota were analyzed by cluster analysis. Results DNA sequence analysis was successfully performed. The Chao 1 index was lower in the group M than group C ( P < 0.05). The Shannon index was lower and the Simpson index was higher in the group M than group C ( P <0.05). At phylum level, the relative abundance of Proteobacteria, Cyanobacteria, Tenericutes, TM7, and Actinobacteria was lower in the group M than group C ( P < 0. 05). At genus level, 4 weeks after injection,the abundance of Lactobacillus was lower and that of Bacteroidetes was higher in the group M than group C ( P < 0.05). 12 weeks after injection, the relative abundance of Lactobacillus,Bacteroides and Ruminococcus was higher and that of Bifidobacterium was lower in the group M than group C ( P < 0.05). Conclusions This STZ?induced diabetic SD rat model has a low abundance and diversity of gut microbiota. Quantitative analysis of gut microbiota composition in this animal model provides a basic data for the study of relationship between diabetes mellitus and gut microbiota.