Abstract: To investigate the interaction between endophytic bacteria and Kandelia candel, root, branch, and leaf samples of K. candel were collected, followed by the extraction of genomic DNA from these samples. The community structure and diversity of endophytic bacteria within K. candel were analyzed utilizing 16S rDNA high-throughput sequencing technology. Additionally, the structural characteristics of endophytic bacterial communities across the various parts of K. candel were analyzed. The results showed that total of 26 phyla, 45 classes, 107 orders, 186 families, and 391 endophytic bacteria were detected, and the total number of OTU was 1893. Proteobacteria occupy the dominant position in the endophytic bacterial community, and Methylbacterium is the most predominant genus in the roots and branches of K. candel, and its relative abundance in leaves is lower than that of Cyanobacteria. The richness of endophytic bacterial communities were root > branche > leaf, and evenness were branch > root > leaf. The dominant bacterial community was significantly correlated with the functions of metabolism, environmental adaptation and genetic information. In conclusion, there were significant differences in the structural characteristics, diversity, dominant bacteria genera of the endophytic bacterial community in roots, branches and leaves, and endophytic bacteria may be an important factors for the excellent adaptability and stress resistance of K. candel.