Objective: To describe the alterations of the composition of vaginal microbiota in pregnant women with COVID-19. Design: Prospective observational single-centre study Setting: Tertiary referral hospital Participants: Pregnant women with COVID-19 Methods: The vaginal swabs were collected during the active phase of infection and consecutively, within a month after recovering from infection. In three patients, longitudinal samples before, in the course, and after infection were also obtained. The microbiome alterations were examined by 16S rRNA gene sequencing. Main outcome measures: Vaginal microbiota profiles in pregnant women with COVID-19 Results: Nineteen pregnant women with COVID-19 and 28 healthy controls who were matched according to the maternal age and gestational week were recruited. Shannon index and inverse Simpson index for cross-sectional cohort indicate that alpha diversity is significantly higher in women with COVID-19 (P=0.007 and P=0.006, respectively). There was a significantly decrease in Firmicutes (P=0.007) and Lactobacillus (P=0.019) with an increase in Bacteroidetes (P=0.024) in women with COVID-19 when compared to those of healthy controls. The higher amounts of Ureaplasma were found in women with the moderate/severe disease, compared to those of the asymptomatic/mild disease (P=0.001). Lactobacillus gasseri disappeared in women with the moderate/severe disease. Prevotella timonensis was identified only in the COVID-19 group. In longitudinal analysis, Actinobacteria was elevated, Firmicutes and Bacteroides depleted during the active phase. Conclusion: The study revealed that vaginal dysbiosis with a low abundance of Lactobacillus and an increase in Bacteroidetes is associated with COVID-19.