Ginger, as a common condiment and traditional Chinese medicine, is one of the important economic plants in China. The plump tuber as a feeding part is closely related to the root system, so the yield and quality of tuber is also deeply affected by the bacteria related to root. However, there are few reports on bacteria in ginger root micro environment, and it is unclear whether the soil environment can derive host specific endophytes. In this research, the bacterial community composition in different niches of ginger (bulk soil, rhizosphere soil, and root) were explored and characterized. The results showed that the alpha diversity (Shannon index, Observed species, and Faith's PD) of bulk soil bacteria and rhizosphere bacteria was significantly higher than that of endophytes. The stability and complexity trend of niche co-occurrence network was bulk soil bacteria > rhizosphere bacteria > endophytes. Bacterial community composition could be significantly separated by niche (R²=0.57, P=0.001). Proteobacteria was significantly enriched in roots. Under this phylum, the dominant bacteria were Pseudomonas, Brevundimonas, Stenotrophomonas and Pantoea etc. Among rhizosphere bacteria, Bacteroidetes and Firmicutes were significantly enriched. The abundance advantage was mainly contributed by Sphingosphaga, Bacillus and Chryseobacterium. Bacterial communities were affected by some soil environmental factors. Soil pH was closely related to bacterial communities in bulk soil. Available phosphorus was significantly related to the composition of rhizosphere bacterial communities, while there was no factor associated with endophytes. Further traceability analysis showed that 42.8% of rhizosphere bacteria originated from bulk soil, while 47.3% of endophytes originated from rhizosphere, which proved that there was niche level transmission in ginger root related bacterial community. In short, the bacterial diversity, stability and categories of bacterial communities in different niches of roots were significantly different, which reflects the screening and filtration effect of roots. By analyzing the composition of bacterial communities in different root niches, the similarities and differences of bacterial communities in different root niches were clarified, which laid a foundation for the development and utilization of ginger root related bacterial communities.