The human microbiome is changing the way experts and non-experts think about germs and microorganisms. This essay is a gender analysis of contemporary discourses surrounding the human reproductive microbiome, specifically the vaginal microbiota and the penile microbiota. I first historically situate the human reproductive microbiome within the germ theory of disease. Then, I draw on Heather Paxson’s Foucauldian and Latourian concept of microbiopolitics to argue that microbiopolitics is not only about how humans should live with microorganisms; but it also impacts (...) how humans and microbes live together as gendered beings. I illustrate this gendering through two figures: the microbial mother and the independent organ. (shrink)