Abstract: Objective To study the microbial community structure on the root surface of patients with periodontitis. Methods Bacterial plaque and tissues from the root neck （RN group）, root middle （RM group） and root tine （RT group） of six teeth with mobility Ⅲ in one patient with periodontitis were sampled. The V3V4 region of 16S rRNA was sequenced on the Illumina MiSeq platform. The microbial community structure was analyzed by Mothur, Qiime and SPSS software. Results The principal component analysis (PCoA) results indicated that the RM samples had a similar microbial community structure as that of the RT samples, which was significant different from that of the RN samples. Thirteen phyla were detected in the three groups of samples, which included 7 dominant phyla. 29 dominant genera were detected in 184 genera. The abundance of Bacteroidetes_［G-6］ and Peptostre ptococcaceae_［XI］［G-4］ had a positive correlation with the depth of the collection site of samples (P<0.05), while the abundance of Prevotella, Selenomonas, Corynebacterium and Olsenella had a negative correlation with the depth of the collection site of samples (P<0.05). Conclusion There is region-specificity of microbial community structure on the root surface of patients with periodontitis.