Background: Culture-independent techniques have made it possible to expand the knowledge about the composition of bacterial communities present in the healthy uterus and their role in health and disease, mainly in humans. However, in animals like mares, there is a dearth of information regarding this area. Aim: To narrow this knowledge gap, the objective of this study was to identify and characterize the composition and function for the uterine microbiome of a group of Chilean purebred mares (CPM), an equine breed with the oldest genealogical record in South America and an economical important reproductive industry. Methods: From uterine biopsy samples obtained during estrus, DNA extraction and targeted sequencing was performed to investigate the bacterial diversity and its probable metabolic function. Results: CPM biopsy samples were characterized by having a varied microbial composition, where the four most relatively abundant phyla were Proteobacteria (69.6%), Firmicutes (21.1%), Bacteroidetes (7.8%), and Actinobacteria (1.06%); which made up 99.6% of the total identified phyla. In contrast, Actinobacteria and Fusobacteria were the phyla not identified in all samples. Of a total of 59 genera identified across all samples, Staphylococcus was the most abundant genus with an average relative abundance of 18.88%, followed by Pseudomonas (17.9%), Escherichia/Shigella (10.42%), and Klebsiella (9.92%). Conclusion: These findings contribute to the knowledge of microbes presence in the uterus, while future studies are required to demonstrate the role of these microorganisms in health and disease.