Abstract: 【Objective】Analyzing the bacterial community structure and diversity, in order to understand the microbial composition rule and explore microbial resources in different ecological niches of selenium watermelon rootassociated microbiome as well as provide theoretical reference for maintaining soil health and microbial ecosystem stability of selenium watermelon. 【Method】Five point sampling method was used to collect soil samples from four ecological niches, including root zone,rhizosphere,rhizoplane and endosphere, labeled as SRW, SRJ, SRB and SRN. The Illumina Miseq sequencing platform was used to analyze the bacterial community in different niches of the selenium watermelon root. The Alpha diversity index of bacterial community were explored, including Sobs, Shannon, Simpson, Chao1, and ACE indexes. Futher, the differences at the phylum and genus levels between each ecological niche, endophytic bacteria and other niches in the selenium watermelon root were compared. Principal coordinate analysis(PCoA) and traceability analysis were performed. 【Result】The results showed that the richness and diversity of bacterial communities in soil(SRW, SRJ and SRB) were significantly higher than those in endophytic bacterial communities(SRN)(P<0.05, the same below). Diversity was ranked by Shannon and Simpson indexes as SRJ>SRW>SRB>SRN, while richness was ranked by ACE and Chao1 indexes as SRW>SRJ>SRB>SRN. The dominant bacterial phyla in the roots of selenium watermelon were Proteobacteria and Actinobacteriota. The proportion of Proteobacteria in all niches ranged from 59.59% to 84.62%. The dominant genera in four niches were Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium,Klebsiella and Azotobacter. The proportion of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium was 5.48%-15.68%. PCoA analysis showed that there were significant differences in the community structure of selenium watermelon root in diffeferent niches(R²=0.6651,P=0.001). There were significant differences in the abundance of 10 bacterial phyla and 8 bacterial genera among the top 15 species in relative abundance of root ecological niches. Among the top 15 species in relative abundance of endophytic bacteria and other ecological niches in the selenium watermelon root, there were significant differences in the abundance of 8 bacterial phyla and 5 bacterial genera. The results of traceability analysis showed that 55.70% of the rhizosphere bacteria came from the root zone, 65.75% of the rhizoplane bacteria community came from the rhizosphere bacteria and 90.75% of the bacteria community inside root came from the rhizoplane bacteria, indicating that there was a certain correlation between the sources of bacterial communities in selenium watermelon root system in different niches. 【Conclusion】Different bacterial communities of Ningxia selenium watermelon are rich in composition, relative abundances are different and bacterial community sourcesb are related, and different niches can select and filter bacterial communities.