This chapter suggests that the female reproductive system (FRS) is anatomically complex with a number of regions each of which supports a distinct microbiota. It helps to understands the important impact that hormonal fluctuations during the menstrual cycle have on the environment of the reproductive system and the consequences of this for the microbial communities that reside there. The chapter explores the profound impact that sexual development, with its accompanying hormonal changes, has on the microbiota of the FRS. Both the anatomy and the physiology of the vagina and cervix are affected by the concentrations and relative proportions of a number of hormones. The chapter shows that dysbiosis of the microbiota of the FRS is associated with the most common disease of women of childbearing age—bacterial vaginosis. The main host-derived source of nutrients for bacteria is cervical mucus. This is supplemented by menstrual fluid in post-menarcheal/pre-menopausal females.