To analyze the feces microbial diversity differences between the tree shrews captured from the wild in Kunming and those after six months of feeding at Kunming Primate Research Center, Chinese Academy of Sciences. Twelve fresh samples of feces were collected to extract total bacterial DNA and used Illumina Miseq platform. The α diversity index analysis showed that there Shannon and Simpson index were no significant difference between the wild and the captive groups(P＞0.05), while the Chao and Ace index were significant different. The PCoA analysis could distinguish the wild group from the captive group, bacterial populations were similar among six tree shrews. At phylum level, the wild tree shrew possessed similar community structure to the captive tree shrews. Firmicutes, Bacteroidetes and Proteobacteria were dominant. At class level, Bacilli and Bacteroidia were dominant in the wild groups, while Bacteroidia, Clostridia and Negativicutes were dominant in the captive groups. Gammaproteobacteria and Negativicutes were found significantly different between two groups(P＜0.05). At order level, Lactobacillales and Bacteroidales were dominant in the wild groups, Bacteroidales and Clostridiales were dominant in the captive groups. Selenomonadales was found significantly differnte between two groups(P＜0.05). At family level, Streptococcaceae and Prevotellaceae were dominant in the wild groups, Prevotellaceae and Veillonellaceae were dominant in the captive groups. Veillonellaceae was found significantly different between two groups. At genus level, Lactococcus and Streptococcus were dominant in the wild groups, Prevotella and Megamonas were dominant in the captive groups. Streptococcus was found significantly different between two groups(P＜0.01), Megamonas was found significantly different between two groups(P＜0.05). Lactococcus in the wild tree shrews was significantly higher than the captive tree shrews. Bacterial populations were similar among the 6 tree shrews. The results prove that the feace flora structure was difference but not significant, indeed the structure of flora has a tendency to complicate in the captive groups.