In recent years, the introduction of advanced technologies has led to a new scientific revolution: the discovery of the human microbiota. Next-generation sequencing allowed the identification of microbial communities in all districts of the human body and, among these, 9% are distributed in the genitourinary system. The microbiota plays a key role in controlling the homeostasis, therefore dysbiosis can lead to an alteration of the physiological state of health. An alteration of female reproductive microbial communities may affect fertility due to an alteration of the vaginal and endometrial ecosystem. A perturbation of the vaginal, cervical or endometrial flora may also have an impact on the outcome of assisted reproductive technology procedures, particularly in vitro fertilization and embryo transfer. This review examines the role of microbiota in human reproduction and its contribution to infertility. In addition we investigate the role of endometrial bacteria in recurrent implantation failure.