AbstractIntestinal microbiota play an important role in the life of amphibians and its composition may vary by developmental stage. In this study, 16S rRNA high‐throughput sequencing was used to profile the intestinal microbiota of Hynobius maoershanensis, which exclusively inhabit the Maoer Mountain swamp at an altitude of approximately 2,000 m. We characterized the bacterial composition, structure, and function of the microbiota of H. maoershanensis at different developmental stages. The alpha diversity was not markedly different for the Simpson, Shannon, Ace, and Sobs indices of microbes. The beta diversity revealed that there were age‐related differences in the structure of the intestinal microbes of H. maoershanensis, specifically, at the phylum level. Bacteroidetes and Proteobacteria were the dominant bacteria present in the adult stage, and the relative abundance of Bacteroidetes was significantly higher compared with that of tadpoles. Firmicutes and Proteobacteria were the dominant phylum during the tadpole stage and their relative abundance was significantly higher compared with the adult period. Functional analysis revealed that the pathways associated with organismal systems and metabolism were significantly enriched in the adults, whereas human diseases, genetic information processing, and cellular processes were more enriched in the hindlimb bud stage. Human diseases and environmental information processing were more enriched in the forelimb bud stage at KEGG pathway level 1. Possibilities for the observed discrepancies include the adaptation to eating habits and the remodeling of the intestines during development. We speculated that H. maoershanensis adults may be more suitable to a high‐fiber diet, whereas the tadpoles are associated with a carnivorous diet. Our study provides evidence of variations in the intestinal microbiota during development in amphibians, highlighting the influence of historical developments on the intestinal microbiota and an increased understanding of the importance of physiological characteristics in shaping the intestinal microbiota of amphibians. These data will help us formulate more effective protection measures for H. maoershanensis.