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In systemic sclerosis (SSc), the gastrointestinal tract (GIT) plays a central role in the patient’s quality of life. The microbiome populates the GIT, where a relationship between the <i>Lactobacillus</i> and gastrointestinal motility has been suggested. In this study, the analysis of oral <i>Lactobacillus</i> species in SSc patients and healthy subjects using culture-independent molecular techniques, together with a review of the literature on microbiota and lactobacilli in SSc, has been carried out. Twenty-nine SSc female patients (mean age 62) and twenty-three female healthy subjects (HS, mean age 57.6) were enrolled and underwent tongue and gum swab sampling. Quantitative PCR was conducted in triplicate using <i>Lactobacillus</i> specific primers <i>rpoB</i>1, <i>rpoB</i>1o and <i>rpoB</i>2 for the RNA-polymerase β subunit gene. Our data show significantly (<i>p</i> = 0.0211) lower <i>Lactobacillus</i>spp<i>rpoB</i> sequences on the tongue of patients with SSc compared to HS. The mean value of the amount of <i>Lactobacillus ssprpoB</i> gene on the gumsofSSc patients was minor compared to HS. A significant difference between tongue and gums (<i>p</i> = 0.0421) was found in HS but not in SSc patients. In conclusion, our results show a lower presence of <i>Lactobacillus</i> in the oral cavity of SSc patients. This strengthens the hypothesis that <i>Lactobacillus</i> may have both a protective and therapeutic role in SSc patients.