The role played by microbiota is attracting growing attention within the scientific and medical community, in both human and animal fields, in the last years. Most of the studies have been focused on the intestinal microbiome, whilst little attention has been paid to other systems, like the reproductive tract of both females and males. However, there is a growing body of information showing the interplay between reproductive tract dysbiosis, due to the action of pathogens and/or unhealthy lifestyle, and reproductive disease and disorders in many mammalian species. The present review aims to summarise current knowledge on the biodiversity of the microbiota of the reproductive tract, and the possible relationships between eubiosis or dysbiosis and reproductive health and function in both females and males.