Abstract: In order to study the bacterial diversity of female donkeys with reproductive disorders, eleven adult female donkeys aged 3-5 years were divided into healthy group（HG group）, uterine inflammation group（MG group） and infertility group（SG group） according to their health conditions. The uterine secretions of each group were collected, and the V3-V4 variable region of bacterial 16 S rRNA was amplified by PCR after total DNA was extracted. High-throughput sequencing was performed using Illumina MiSeq PE300 platform. Statistical analysis and OTU clustering were performed on sequencing data, and dilution curves were drawn. Alpha diversity index（Chao, Ace, Shannon, Simpson and Coverage index） was calculated. Species annotation and statistics were performed based on OTU clustering results, and differences in Beta diversity and relative abundance of flora were analyzed. The results showed that a total of 436 487 valid sequences were obtained, including 152 882 sequences in HG group, 161 781 sequences in MG group and 121 824 sequences in SG group. The effective sequence length mainly ranged from 421 to 460 bp, with an average of 437 bp, including 437 bp in HG group, 438 bp in MG group and 436 bp in SG group. The number of OTUs was 511 according to 97% similarity level of sequences. Ace and Chao indexes in SG and MG groups were higher than those in HG group. The Shannon index was highest in SG group and lowest in MG group. Simpson index was the highest in MG group and the lowest in SG group. The Coverage index of the three groups was 0.99. There were 10 phyla with relative abundance higher than 1% in the three groups, accounting for 95.74%-97.98% of the relative abundance of bacteria. They were Bacteroidetes, Firmicutes, Proteobacteria, Actinobacteria, Fusobacteria, Synergistetes, Saccharibacteria, Spirochaetae, Absconditabacteria＿SR1 and Tenericutes, and the dominant bacteria were Bacteroidetes, Firmicutes, Proteobacteria and Actinomycetes. There were 37 genera with relative abundance higher than 1% in the three groups, accounting for 66.60%-78.67% of the relative abundance of bacteria. They were Porphyromonas, Filobacterium, Campylobacter, Fusobacterium, Oceanivirga, Corynebacterium, Peptoniphilus, Ezakiella, Mobiluncus, Peptostreptococcus, etc. The dominant bacteria were violet Omonas, Filamentous bacillus, Campylobacter and Clostridium. PCA analysis showed that the difference in flora composition on the PC1 axis of HG group, MG group and SG group was 48.54%, and that on the PC2 axis was 15.02%. PCoA method was used to analyze the difference of flora composition on the PC1 axis of HG group, SG group and MG group, and the difference of flora composition on the PC2 axis was 37.76% and 23.44%, respectively. The flora composition of the three groups was similar on the whole, but the community composition of individual samples in MG group differed greatly from that of other samples. The relative abundance of Ciliomycetes in HG group was the highest among the three groups, which was significantly different from the other two groups（P＜0.05）. The relative abundance of Corynebacterium and Christensenia in SG group was the highest among the three groups, which was significantly different from the other two groups（P＜0.05）. The relative abundance of Bacteroidetes in MG group was the highest among the three groups, which was significantly different from the other two groups（P＜0.05）. The results indicated that the diversity of bacterial community in uterus of female donkeys under different health conditions was significantly different.