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Bacterial vaginosis (BV) is the most common vaginal infection globally, with a high recurrent rate after antibiotic treatment. Probiotics consumption is known to improve BV with different efficacy among species or strains. After in vitro selection of <i>Lactobacillus</i> strains with growth inhibition and preventing adhesion to HeLa cervical epithelial cells, a randomized and double-blinded trial of two <i>Lactobacillus</i> formula, namely, VGA-1 and VGA-2, in BV patients with Nugent scores of 4–10 was conducted. Among 37 subjects who completed the trial, we observed significantly decreased Nugent scores in both VGA-1 (<i>n</i> = 18) and VGA-2 (<i>n</i> = 19) consumption groups. VGA-1 consumption significantly improved vaginal discharge odor/color and itching at both 2-week and 4-week-consumption, but those only observed after a 4-week-consumption in the VGA-2 group. We also observed a tendency to reduce recurrent rates among enrolled participants after VGA-1 or VGA-2 consumption. The improvement effect of VGA-1/VGA-2 was associated with the significant reduction of interleukin-6 expression after 4-week-consumption and the restoration of normal vaginal microflora by quantitative polymerase chain reaction analysis. In conclusion, VGA-1 or VGA-2 displayed beneficial effects in BV patients, but the VGA-1 formula showed a better efficacy, potentially used for BV intervention.