ABSTRACT Introduction: There are no molecular data regarding the composition of the vagina and gut microbiome of Nigerian women with bacterial vaginosis (BV), mostly due to lack of appropriate application of high throughput sequencing methods. Here, we aimed to characterize and compare the vaginal and gut microbiome of women with bacterial vaginosis. Material and Methods: Bacterial vaginosis was initially diagnosed using the Nugent scoring method among 220 women aged 18 to 45 years. Five BV positive samples (vagina and gut) were randomly selected and sequenced with Illumina MiSeq platform for the 16S rRNA V4 region using custom-barcoded primers. Alpha-diversity was estimated for species richness by ACE, Chao1 and Jackknife method, while the diversity index was calculated by Shannon, Non-parametric Shannon, and Simpson index. For beta-diversity, Jensen-Shannon metrics were used for principle coordinates (2D) analysis at the species level. Results: Nugent scoring method showed 43 (19.5%) of the subjects had BV. The Shannon diversity index for vagina and gut samples for Subject 1, 2, 3, 4 and 5 was 2.51/3.76, 1.96/3.18, 0.28/4.69, 1.67/3.14, 1.58/3.94 respectively. The average distribution of phyla, class, order, family, genera, and species in the vaginal microbiome was 9.4, 16.8, 31.2, 63.8, 109 and 161.4 respectively whereas, in gut microbiome it was 19.6, 34.2, 68.8, 136.2, 274.4, and 410.8 respectively. Relative abundance showed Firmicutes followed by Actinobacteria, Proteobacteria, dominated the vagina while gut microbiome was dominated by Firmicutes followed by Bacteroidetes, and Proteobacteria. The phylogenetic diversity of the vagina was significantly lower than that of the gut. However, 12 genera out of 20 associated with BV were recovered from both niches with different abundance among the subjects. Functional prediction using PICRUSt and LEfSe revealed significant differences between the vagina and gut microbiome in the relative abundance of microbial genes related to some metabolic pathways. Conclusion: This is the first study using metagenomics in Nigeria that has provided an insight into the phylogenetic diversity and species richness of the vagina and gut microbiome of reproductive age women with BV. In addition, the study revealed relative abundances of microbial genes associated with metabolic functions that are upregulated in the vagina and gut of BV subjects.