Camellia chrysantha is cultivated as rare genetic resource of the family Theaceae, which mainly distributed in the South of Guangxi Zhuang Autonomous Region in China. Rhizosphere microbiota may play important roles in C. chrysantha growth and homeostasis through interaction of the plant and soil ecosystem. In order to investigate the bacterial community composition in the rhizosphere soil of three C. chrysantha cultivars under different growing conditions, Illumina MiSeq high-throughput sequencing and real-time quantitative PCR methods were used in this study. Results indicated that Proteobacteria, Acidobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and Gemmatimonadetes were the top six phyla across all the six rhizosphere soil samples. The richness and diversity of bacterial community in the rhizosphere soil from cultivar “Fangpu” grown understorey (LF) in retail planting area were significantly different from the other samples. Principal coordinate analysis revealed that bacterial community composition of the rhizosphere soil from cultivar “Fangpu” grown understorey (LF) and perennial grown undershed (PFC) was obviously separated from each other as well as the other four rhizosphere soil samples. The growing conditions displayed more influences on the bacterial community composition than plant cultivars, and close correlations were found between the soil physicochemical characters of the geographical origins and the bacterial communities. This work improves understanding of the rhizosphere bacterial community composition and the influencing soil physicochemical factors, and provides basic information for cultivation and protection of the C. chrysantha plants in China.