Gut microbiota regulate the material and energy metabolism of organism and participate in immunity and disease prevention, which is helpful to maintain the normal physiological activities of animals. Aix galericulata was selected to explore the possible mechanism of microbiota- inducing enteritis in birds. Two scientific questions were concerned: 1) which (several) bacteria may induce enteritis in A. galericulata? What kind of pathogenic mechanism may cause enteritis in A. galericulata? High-throughput sequencing was utilized to analyze the gut microbiota of both healthy animals and those with enteritis, and comparisons were carried out on the diversity and composition between the two groups. A total of 2020 97% operational taxon units (OTUs) were identified from the gut microbiota of A. galericulata. The number of common OTUs in healthy group and enteritis group was 564 (Fig. 2). The alpha diversity index of healthy group was higher than that of enteritis group, but without significance (P > 0.05). At phylum level, Firmicutes (73.46%), Bacteroidetes (11.15%) and Proteobacteria (8.72%) were the main compositions of the gut microbiota in A. galericulata (Fig. 3). At genus level, Kurthia (24.74%) and Lactococcus (8.47%) were the most abundant taxa in healthy group, and Clostridium sensu stricto 1 (29.65%) and Lactobacillus (12.40%) were main components in enteritis group. There is significant difference in gut compositions between healthy group and enteritis group (P < 0.05). In the enteritis group, a total of 25 microbial classifications were found significantly higher than those of healthy group. Among them, Clostridium_sensu_stricto_1, Escherichia-Shigella and Desulfovibrio bacteria are the most abundant (liner dicriminant analysis value > 5, P < 0.05) (Fig. 6). Clostridiales, Desulfovibrionaceae and Bacillales play important function in the gut of A. galericulata (Fig. 7). The conclusion is that the high contents of Clostridium_sensu_stricto_1, Escherichia-Shigella and Desulfovibrio may destroy the balance of intestinal microbial community, cause the decline of immunity, and then serve as important factors inducing the enteritis of A. galericulata.