Background: Children with craniofacial dysmorphism are at higher risk of the presence of mouth breathing (MB), which is associated with alterations in the oral microbiome. These children often undergo orthodontic therapy, which can improve their condition, but also constitutes a risk factor for oral dysbiosis. Objective: To compare the bacteriomes of the dorsum of the tongue in children with/without MB before and during orthodontic treatment. Methods: In this pilot prospective case-control study, we matched 15 children with MB and 15 children without MB, according to age, sex and BMI. The Czech and Slovak children, aged 7-12 years, were from the pool of patients from a single orthodontic department, and all children were examined by the same orthodontist. Tongue swabs were collected before the orthodontic therapy (M0) and during the treatment, approx. 6 months after the start (M6). DNA was isolated from 60 samples. All samples and negative controls (DNA-free water) were spiked by a commercial mock community and QIAmp DNA Mini Kit and 16S rRNA amplicon sequencing on the Illumina MiSeq platform was performed. Results: There were no significant differences in alpha or beta diversities of bacterial genera between the MB and NB groups before or during the treatment (p>0.05). Streptococcus, Prevotella, Veilonella, Neisseria, Rothia, and Haemophillus were the most abundant genera. Before the start of the orthodontic therapy, we observed a significantly higher relative abundance of the genus Solobacterium in children with MB than in children with NB (q=0.012, Dunn's test). Conclusion: The bacteriomes of the dorsum of the tongue did not significantly change in relation to the orthodontic therapy and were similar in children regardless of whether they are mouth breathers or breathe normally. Nevertheless, our findings showed that the oral presence of the genus Solobacterium (previously associated with halitosis) can be related to MB.