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[Objective] In the present paper, the community diversity of endophytic bacteria in different parts of Panax notoginseng was studied.[Method] High throughput sequencing technology was used to sequence the region V5-V7 of 16 S rRNA gene of Panax notoginseng endophytic bacteria, and bioinformatics analysis was carried out for the diversity of endophytic bacteria in different parts of Panax notoginseng. [Result] There were 385,206 and 226 OTUs which were obtained from the roots, stems and leaves of Panax notoginseng, respectively. Total of 167 OTUs were the same in the three parts, accounting for 19.04%.The results of taxonomic species classification showed that endophytic bacteria in leaves belonged to 16 phyla, 27 classes, 74 orders, 134 families, 222 genera, and the dominant genera were cutibacterium and Ralstonia, accounting for 28.70% and 14.57%,respectively; endophytic bacteria in stems belonged to 12 phyla, 20 classes, 58 orders, 108 families, 178 genera, and the dominant genera were Pseudomonas, accounting for 45.50%;Endophytic bacteria in roots belonged to 19 phyla, 24 classes, 75 orders, 137 families, 202 genera, and the dominant genera were Burkholderia-caballeronia-paraburkholderia and Escherichia-Shigella, accounting for 24.78% and 21.94% respectively. It could be seen that the species richness of the roots was higher than stems and leaves.[Conclusion] Endophytic bacteria in different parts of Panax notoginseng were rich in community diversity, but the abundance of different parts was different. The abundance of different parts displayed as root > leaf > stem, and the dominant genera in different parts were different. The partial bacterium of dominant genera had some functions, which could be further developed and utilized. The research of endophytic bacteria diversity in different parts of Panax notoginseng will lay a foundation for screening of biocontrol strains. [ABSTRACT FROM AUTHOR]