The gut and skin play important roles in the body's immune system and are often exposed to the external environment. The difference in microbial communities can reflect the changes of the host in response to different environmental conditions. Whilenumerous gut and skin microbia have been characterized, there is no comparative analysis of the gut and skin microbial communities in the amphibian. In our study, we examined the difference of gut and skin tissues of Rana chensinensis tadpoles by hematoxylin-eosin (H.E) and Masson staining. Furthermore, we investigated the difference of gut and skin microbial communities in R. chensinensis tadpoles at Gosner stage 38 by using high-throughput 16S rRNA sequencing technology. The statistical significance of difference was determined by the Student’s T-test. Our results revealed that: (1) There were histological structure difference of gut and ventral skin in tadpoles (Fig. 1). (2) The alpha diversity analysis showed that the microbial community biodiversity in the gut was significantly higher than that in the skin (P ≤ 0.001), while there was no difference in community richness between gut and skin samples (P > 0.05; Fig. 3). In addition, the hierarchical cluster and PCoA analysis showed that the distance of microbial communities between these two tissues was clearly separated from one another (Fig. 4). (3) Venn diagram showed that 175 OTUs were shared bythe gut and skin, while 70 OTUs were independently presented in the gut, and 87 in the skin (Fig. 5). (4) A taxonomic analysis revealed that the most prevalent phyla in the gut were Bacteroidetes, Proteobacteria and Verrucomicrobia, whereas the predominant phyla found in skin were Proteobacteria, Firmicutes and Bacteroidetes (Fig. 6a). Moreover, the Student’s T-test results revealed that the abundance of Firmicutes and Actinobacteria in the gut was significantly higher than in the skin, while the abundance of Bacteroidetes was just significantly higher in the skin (P ≤ 0.05; Fig. 6b). (5) The functional prediction results indicated that the abundance of “environmental information processing” function was significantly higher in the gut, whereas the “genetic information processing” and “metabolism” functions were significantly higher in the skin (P ≤ 0.01; Fig. 9). The results of this study revealed that there were significant differences in the composition of microbial communities in the gut and skin of R. chensinensis tadpoles. These differences will promote the growth and development of tadpoles to adapt to environmental changes.