Abstract: In this study, the structural characteristics of endophytic bacterial communities in different parts of Kandelia candel were analyzed to explore the interaction between endophytic bacteria and K. candel, and to provide references for the full development of endophytic bacterial resources in K. candel.The tissue sample of roots, branches, and leaves of the K. candel were collected, the genomic DNA of the samples was extracted, and the community structure and diversity of endophytic bacteria were analyzed by 16S rDNA high-throughput sequencing technology. 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 of Lycopodium, and Methylbacterium is the most dominant 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 roots > branches, > leaves, and evenness were branches > roots > leaves. 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 and marker bacteria of the endophytic bacterial community in roots, branches and leaves, and endophytic bacteria maybe an important factors for the excellent adaptability and stress resistance of K. candel.