Objective:To summarize and compare the characteristics of oral microbiota in women during the preconception period and the third trimester.Methods:This retrospective cohort study involved 55 women who were recruited in the Preconceptional Offspring Trajectory Study (PLOTS) conducted by Fudan University and followed up to the third trimester in the Maternal and Child Health Care Hospital of Jiading District of Shanghai from September 2016 to December 2019. A total of 110 unstimulated saliva samples were collected in the preconception period ( n=55) and the third trimester ( n=55). Features of oral microbiota in the samples were analyzed by 16S rRNA gene-based sequencing. Moreover, the related factors were also analyzed. Paired t test or Wilcoxon matched-pairs signed-ranks test were used to analyze the differences in α-diversity during preconception and the third trimester; t test, analysis of variance (ANOVA), Kruskal-Wallis test and Mann-Whitney U test for comparison between groups with different characteristics and permutational multivariate analysis of variance (PerMANOVA) for β-diversity were used; Linear discriminant analysis (LDA) effect size (LEfSe 1.0) was used to identify the iconic oral flora. Results:(1) The Ace index of oral microbiota was significantly lower in the third trimester than that in the preconception period [661.14(578.15-752.85) vs 730.64 (632.40-911.00), T=1 077.00, P=0.010]. There was also a significance difference in β-diversity ( F=12.539, R2=0.104, P=0.001). Some species such as Saccharibacteria_TM7_G3, Prevotella_7, Absconditabacteria_SR1_G1, Porphyromonas, Ruminococcaceae_UCG_014, Prevotella, Peptostreptococcus, Prevotella_2, Alloprevotella, Parvimonas, Solobacterium and Eubacterium_nodatum_group in saliva were statistically more abundant in the third trimester than those in the preconception period (all P<0.05). (2) The third-trimester Shannon index was lower among those with lower income [5.44 (5.08-5.77) vs 5.75 (5.44-6.12), U=219.00, P=0.029] and those with gargle habit after meal or dessert [5.36 (4.91-5.48) vs 5.72 (5.44-6.05), U=374.00, P=0.046]. Conclusions:The features of oral microbiota vary in women during the preconception period and the third trimester. There is a significant increase in the abundance of oral pathogenic and opportunistic bacteria in the third trimester.