Objective To assessment of the composition and ecology of the vaginal microbial ecosystem in asymptomatic women. Design Microbial monitoring of reproductive tract and human papillomavirus (HPV) infection. Population Healthy women of childbearing age. Setting China Methods The relationships between HPV infection and vaginal, cervical and gut microbiota composition and the levels of genital immune mediators were assessed. We selected a multiethnic area in Yunnan Province, China to collect samples from healthy women of childbearing age. Vaginal, cervical and rectal swabs were collected to analyze the microbial community, and cytokines were analyzed in some samples. Main outcome measures Different proportions and types of HPV infection were detected in vaginal (18%), cervical (44%) and rectal (18%) swabs. Results There were some differences in this proportion as well as in the microbial community composition among different ethnic groups. Rectal samples exhibited the highest diversity index, while vaginal samples displayed the lowest diversity index. Lactobacillus dominated most of the vaginal samples, was decreased in HPV-positive samples, and differed among different ethnic groups. However, the sequence proportion of Lactobacillus in the cervix exhibited the opposite trend in those affected by HPV infection. The dynamic balance between the potential pathogens Gardnerella and Lactobacillus determines the health of the female genital system. Conclusions This study constitutes the first step toward personalized medicine for women’s reproductive health, wherein differences between the genital microbiomes of individuals would be considered in risk assessment and for subsequent disease diagnosis and treatment.