Objective To analyze the differences in fecal microflora composition between normal and diarrheal forest musk deer in captivity, find out the marker bacteria that could affect the stability of total intestinal microflora, and provide new strategies for reducing diarrhea incidence in forest musk deer. Methods The 16 S rRNA gene V3-V4 region of total DNA of intestinal microflora was sequenced and analyzed in 54 healthy musk deer and 18 forest musk deer with diarrhea symptoms. The Chao1, Ace, Shannon and Simpson were calculated, and the distance clustering anal. was carried out. Results There were 2, 366 OTUs shared between normal control group and diarrhea group, 409 OTUs specific to normal control group, and 150 OTUs specific to diarrhea group. The levels of Chao1 and Ace in diarrhea group were higher, while Shannon and Simpson were lower than those in normal control group resp. Wilcoxon rank sum test showed the intergroup difference was greater than the intragroup difference(all P<0.01). At phylum level, five different species were found, which were Bacteroidetes, Spirochaetes, Actinobacteria, Euryarchaeota and Melainabacteria. At genus level, 23 different species were found; the representative species were Bacteroides, Aristipes, Agathobacter, Methanobrevibacter, Rhizobiaceae and Chryseobacterium. Conclusion The abundance and diversity of intestinal microflora of musk deer decreased and the total amount of intestinal microflora increased significantly when diarrhea occurred. While the species richness of Bacteroides decreased significantly, the proportion of Proteobacteria as a potential pathogen increased, and the number of Chryseobacterium increased significantly.