Simple SummaryGolden snub-nosed monkey is a critically endangered primate. Determining the gut microbial diversity, construction, and function is vital for protecting the golden snub-nosed monkey. The gut microbiota plays an essential role in regulating the physiological health of wild animals. The dominant phyla in the gut microbiota of captive and wild golden snub-nosed monkeys areBacteroidetes,Firmicutes, andKiritimatiellaeota. There are significant differences in the alpha and beta diversities of the gut microbiota between wild and captive golden snub-nosed monkeys, with the captive population having higher alpha diversity than the wild population. Functional predictions related to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database showed that the most significant functional pathway at the second level between captive and wild monkeys was carbohydrate metabolism.AbstractEnvironmental shifts and dietary habits could directly affect the gut microbiota of animals. In this study, we investigated the gut microbiota of golden snub-nosed monkeys under two different conditions: captive and wild. Our study adopted a non-invasive sampling method, using full-length 16S rRNA Pacbio SMAT sequencing technology to compare the gut microbiota of wild and captive golden snub-nosed monkeys. The results showed that the captive populations had higher alpha diversity than the wild populations, and there were also significant differences in beta diversity. The linear discriminant analysis effect size (LEfSe) analysis showed 39 distinctly different taxonomic units. At the phylum level, the most dominant bacteria under captive and wild conditions were Bacteroidetes and Firmicutes. This study revealed that the different fiber intake between wild and captive populations might be the main reason for the difference in the gut microbiota. We found that captive golden snub-nosed monkeys had less beneficial bacteria and more potentially pathogenic bacteria than wild ones. Functional predictions showed that the most significant functional pathway at the second level between the captive and wild monkeys was carbohydrate metabolism. Therefore, our results indicate that diet changes caused by captivity could be the main reason impacting the gut microbiota of captive golden snub-nosed monkeys. We further highlight the potential impact of diet changes on the health of captive golden snub-nosed monkeys and offer some suggestions for the feeding of captive golden snub-nosed monkeys.