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Dental caries remains a public health threat of concern among children. About 2.3 billion people are affected by dental caries, of which 530 million are children globally.This study was carried out to identify sugar fermenting bacteria in the oral cavity and their antibiotic susceptibility pattern, assess the association with sugar fermenter bacteria and dental caries and evaluate dental caries outcomes among children.This was a cross-sectional study conducted between October 2021 and February 2022 at Ruhengeri Referral Hospital. About 136 oral swab samples were collected from children with and without dental caries at 1:1 ratio. The samples were put in Stuart sterile container and transported to INES-clinical microbiology laboratory for microbial identification. Logistic regression analysis of demographic characteristics was performed to study the relationship between demographic variables and dental caries. Chi-square test was performed for the association between variables.About 67.6% were male, while children of age 7-9 years (64.7%) dominated the age groups. Lactobacilli spp (15.29%) and Streptococcus mutans (12.94%) were the most predominant microorganisms observed in the oral cavity among children with dental caries. The S. mutans (xSugar consumption favours the growth of sugar fermenter bacteria that cause dental caries among children. Dental caries is associated with adverse oral health outcomes among children. Oral health education is recommended for children. Parents are advised to reduce the consumption of sugary food for their children for oral health safety.