Objective Study the fecal flora diversity of the tree shrew, to provide a basis data of fecal bacteria of feeding the tree shrew. Methods Ten tree shrews were used in this study. The Stools of the animals were respectively cultured with oxygen and without oxygen to isolate the bacterial. Then the PCR-amplified 16S rRNA of the bacterial was sequenced and analyzed. Results 25 bacterial strains belonging to ten bacterial species were isolated by anaerobic incubation, and 25 bacterial strains belonging to twelve bacterial species were isolated by aerobic incubation. Proteus vulgaris, Enterococcus faecalis, Escherichia fergusonii, Enterococcus faecium, Shigella flexneri, Shigella sonnei, Staphylococcus aureus, Aeromonas salmonicida subsp.masoucida, Rahnella aquatilis, Exiguobacterium aquaticum, Raoultella terrigena, and Escherichia coli were identified in this study. Conclusions There is a fecal flora diversity of the tree shrew, and the Proteus vulgaris, Escherichia fergusonii and Enterococcus faecium may be the major parasitic flora.