Objective To analyze the structure and composition of intestinal flora in the common cotton-earedmarmoset using the Illumina MiSeq sequencing platform. Methods Feces of the common cotton-eared marmoset werecollected and investigated for microbial diversity using the Illumina MiSeq sequencing platform. Results In total, 315511sequences and 596 OTUs were obtained after sequencing. According to the Shannon-Wiener curve, the sequencing datawere reliable for all bacteria in the samples. The bacteria in the common cotton-eared marmoset included 9 phyla, 14classes, 26 orders, 50 families, 82 genera, and 64 species. Among them, Firmicutes and Bacteroidetes had the highestabundance (54. 52% and 25. 39%, respectively). The dominant classes were Bacteroidia and Negativicutes at 54. 5% and17%, respectively. The abundance of Lactobacillales and Bacteroidales was higher at 50. 01% and 20. 52%, respectively.Dominant families were Prevotellaceae and Bifidobacteriaceae at 43. 14% and 11. 33% respectively. Lactobacillus andStreptococcus were dominant at 20. 03% and 19. 62%, respectively. The abundance of beneficial bacteria, such asBifidobacterium, was high, which were found in samples. The top 10 species with the highest abundance were classified intoseven families and five classes. These 10 species accounted for 33. 16%, and the other 53 species only accounted for0. 74%. Other species were not identified, and the abundance was relatively high, which require further study. PICRUStfunctional prediction showed an abundance of functional genes such as those involved in amino acid transport andmetabolism as well as genetic information processing. Conclusions The composition of fecal microbiota in common cottonearedmarmoset has rich diversity. Many bacteria that are relatively abundant remain unidentified, and further study is warranted.