With the advent of omics technology and the improved culturing of anaerobic microbes, there is a good understanding of the microorganisms present in a healthy and diseased vagina. This has led to the identification of a select few Lactobacillus species associated with health. However, the origin of these species and how they reach the vagina remains unclear, as does their timing of colonization. In an effort to create badly needed therapies for women, these gaps in knowledge need to be addressed.