Red Panda Ailurus fulgens which depends heavily on bamboo with high fiber content, like Giant Panda Ailuropoda melanoleuca, retains the similar digestive system with carnivore. The purpose of our research is to determine the microbial structure of the feces of Red panda, and explore the biological mechanism of the bamboo feeding habits. Feces of captive Red pandas from Hangzhou zoo and Shanghai zoo were collected, and Hiseq high-throughput sequencing based on 16S rRNA gene was conducted to determine the structure of fecal microbiota of Red panda. For the diversity of microbiota composition, Sobs, Shannon, simpson, ace and Chao1 index were calculated. Wilcoxon rank-sum test was used to evaluate the influence of diet composition and age on the microbiota structure. Tax4Fun was used to predict the function of microbiota. The results showed that the diet compositions influenced the microbiota diversity of Red pandas (P < 0.05), and the microbial diversity of adult Red pandas was significantly higher than that of cub and old groups (P < 0.05) (Table 2). The fecal microbiota of the Red panda was mainly composed of Firmicutes, Proteobacteria and Bacteroides at phylum level, and composed of Eschericia-Shigella, Clostridium sensu stricto and Enterobacter at genus level (Fig. 2). For the fecal microbiota of Red panda, the metabolic genes related to carbohydrates and amino acids were the richest, followed by the metabolic genes related to energy and lipid (Fig. 5). 6-phosphate-β-glucosidase and β-glucosidase might be helpful for the digestion of high fiber diets (Fig. 6). The microorganisms of Red panda can be helpful in metabolizing carbohydrates and amino acids, and producing enzymes to digest cellulose.