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Bacterial communities in the mammalian reproductive system can be rich and diverse, differing in structure and quantity depending on location. In addition, its microbiome is associated with the state of health of this tract and reproductive success. This study evaluated the microbiome composition of the uterine body (UB) and uterine horn mucosa (UH) samples using 16S rRNA sequencing of samples extracted from cows in the Amazon region. It was observed that four main phyla were shared between the uterine sites: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Linear discriminant analysis effect size and heat tree analysis showed that members of Lachnospiraceae (NK3A20 group) and Oscillospiraceae were significantly more abundant in the UB than in UH. In addition, there are more unique genera in the UB than in the UH. A higher bacterial load in UB than in UH is expected because of the exposure to external factors of UB. However, comparing the site's communities through beta diversity did not generate well-defined clustering. Thus, it can be attributed to the closeness of the sites, which would make the niches similar ecologically and microbiologically. Therefore, this research provides knowledge to understand biomarkers in the prior reproduction period. [ABSTRACT FROM AUTHOR]