It is necessary to understand the microbial interactions with this plant to study the effect of its medicinal quality. In the present study, high-throughput sequencing was used to analyze the diversity of endophytic bacteria on leaves, branches and fruits of C. grandis cv. Tomentosa. This study obtained a total of 607,952 high-quality sequence fragments of the V3-V4 region from nine samples that belonged to three groups, and 382 operational taxonomic units. The diversity of endophytic bacteria is high while occurrence was different in fruits, branches and leaves. There were 191 OTUs in the three groups. Candidatus Liberibacter was the most abundant class in branches and fruits, while the dominant population of leaves was Massilia. The 16S rRNA function prediction was taken to understand the function of C. grandis cv. Tomentosa. All results not only have reference signifi cance for the functional study of endophytic fungi and the utilization of endophytic fungi, but also have reference signifi cance for the biological control of plant diseases on C. grandis cv. Tomentosa.