OBJECTIVE: The primary objective of this study was to scrutinise the disparities in the diversity, structure, and function of the oral microbiome among caries-free children from the Zhuang and Han ethnic groups with a focus on the influence of ethnically distinct oral health behaviours on the composition of the oral microbiota. METHODS: A questionnaire survey was conducted to assess oral health behaviours and dental plaque samples were collected from 96 Zhuang and Han children aged 4-5 years living in Guangxi, southern China for high-throughput sequencing. PCR amplification was performed for sequencing of the V4 region of the 16S rDNA gene, and second-generation sequencing was performed using the Illumina MiSeq platform to compare and analyse the diversity, structure and function of the microbiota. RESULTS: Single-factor analysis revealed significant differences between the Zhuang and Han ethnic groups regarding juice consumption, the frequency of consuming sugar-sweetened food or beverages before bedtime, the age that individuals started toothbrushing, the frequency of toothbrushing and the frequency of parental assistance with toothbrushing ( < 0.001). The dominant phyla were , etc., and the dominant genera included and . The dental plaques of the caries-free Zhuang and Han ethnic groups had similar core microbiomes, with no significant differences in the diversity and structure of the microbiota and no significant differences in the abundance of the dominant genera. In addition, no significant difference in metabolic function was observed between the Zhuang and Han ethnic groups. CONCLUSION: The core oral microbiota was consistent in caries-free Zhuang and Han children. Despite differences in dietary habits and oral hygiene behaviours between the Zhuang and Han ethnic groups, with a high frequency of sugary food intake but better oral health behaviours in the Zhuang group, there were no significant differences in the diversity, structure and function of the oral microbiota of caries-free children in the Zhuang and Han ethnic groups.