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Objective. To identify the microbiota communities in the vaginal tracts of healthy Mexican women across the pregnancy. Methods. Vaginal swabs were obtained during the prenatal visit of women from all trimesters (n = 64) of healthy pregnant women of Mexico City. DNA was isolated from each sample, and PCR-DGGE and sequencing of 16S rRNA gene fragments were used to identify the bacterial communities. Results. 21 different microorganisms were identified in the vaginal samples. Lactobacillus genus was present in 98% of women studied. Four lactobacilli species were identified in vaginal samples. L. acidophilus was the predominant (78%) followed by L. iners (54%), L. gasseri (20%), and L. delbrueckii (6%). 17 different microorganisms related to bacterial vaginosis conditions were identified. Ureaplasma urealyticum was the predominant (21%) followed by BVAB1 (17%) and Gemella bergeriae (7.8%). Conclusions. Lactobacillus genus predominates in the vaginal samples of Mexican pregnant women associated with different microorganisms related to bacterial vaginosis conditions.