The cervico-vaginal microbiota (CVM) has a huge potential to influence female reproductive health. However, ever since the MetaHIT and the HMP consortia, the microbiome field has mostly been generating data on the fecal microbiome, while the investigation of the CVM has lagged behind. For the CVM, PCR or 16S rRNA gene amplicon sequencing studies have been centered around bacterial dysbiosis and relevant risks of diseases, but a comprehensive view of the microbiota including bacteria, archaea, viruses, and fungi, as well as the functional capacity encoded is largely unknown. Besides infections, little attention has been paid to much larger general population. Thus, my Ph.D thesis has focused on investigating the CVM in healthy Chinese women (Study I and II) utilizing metagenomic shotgun analysis. The Study III is a continuation of my previous work (Chen et al., 2017), which is about the female urinary microbiota. As is known, urine originates from the part of urogenital system and is very close to women’s vagina, So, the particularly interests are whether the urine harbors distinct microbial communities, and how the microbiota within female reproductive tract influence the urine microbiota. To address these questions, I characterized the urinary microbiota and its relationship with the microbiota in the multi-sites of the female reproductive tract. Additionally, I studied on a unique model (neovagina) for exploring microbiota assembly (Study VI).