To investigate the effects of endophytes on rhizosphere soil fertility of the endemic Chinese plant Pteroceltis tatarinowii, the common native tree species P. tatarinowii in northwest Guangxi Zhuang Autonomous Region and the pioneer tree species of the stone mountain afforestation, Zenia insignis, were selected as research subjects. Non-rhizosphere soil samples, rhizosphere soil samples and root samples of P. tatarinowii from natural vegetation plots and Z. insignis from plantation control plots were collected as experimental materials, using the conventional methods of soil physical and chemical analysis, bacterial culture and 16S rRNA sequencing, the community structure characteristics of non-rhizosphere soil bacteria, rhizosphere soil bacteria and root endophytic bacteria of tree species were analyzed respectively. The correlation between root endophytic bacteria and soil physical and chemical factors was analyzed at two different levels of phyla and genera, which further explained the effect of endophytic bacteria on the changes of soil fertility of P. tatarinowii rhizosphere. The results showed that: (1) there were significant differences in bacterial populations among different vegetation plots, whether it was non-rhizosphere soil bacteria, rhizosphere soil bacteria or root endophytic bacteria, the contrast plots of Z. insignis plantation were obviously higher than that of the natural vegetation plots of P. tatarinowii; (2) root endophytic bacteria, rhizosphere soil bacteria and non-rhizosphere soil bacteria were related to each other and interacted with each other. There were not only certain number of common species, but also their own unique species, and the number of unique species was obviously larger than that of common species; (3) in different vegetation plots, the order of microflora was rhizosphere soil bacteria>non-rhizosphere soil bacteria>root endophyte; (4) the dominant phyla composition of soil bacteria and root endophytic bacteria were similar, but their relative abundances were different. The dominant flora of common species of P. tatarinowii was Bacillus, most species of this genus could improve the growth environment of plants to some extent, and enhance the ability of plant resistance to adversity and disease. Therefore, the root endophytic bacteria of P. tatarinowii, like those of Z. insignis and other plants, improve the rhizosphere soil fertility to a certain extent.