Technical Abstract: The analyses methods of Pearson correlation coefficient (PCC), hierarchical cluster analysis and diversity index were used to study the relevance between citrus huanglongbing (HLB) and the endophytic bacteria in different branches and leaves as well as roots of huanglongbing (HLB)-affected citrus trees. The results showed that 26 isolates (10 isolates from leaves, 14 isolates from branches and 2 isolates from roots) from HLB-affected citrus plants belonged to 19 bacterial species in 10 Genus. Among the 12 tested leaf samples, 58. 3% of them were positive for the HLB pathogen using Nested-PCR. The numbers of endophytic bacteria in the different parts of citrus plants ranked as in citrus root > in leaves > in sticks using statistical LSD (least significant difference). The numbers of endophytic bacteria in leaves with different orientations were significant different but little difference were found among upper parts, middle parts and lower parts. Among the bacterial populations, Bacillus pumilus and Bacillus sp. were significantly negatively correlated to HLB bacterium; Bacillus sp. and Bacillus pumilus was positively correlated to Bacillus subtilis, while Bacillus brevis and Escherichia hermannii was positively correlated to Bacillus vesicularis. Furthermore, there was no correlation between Bacillus subtilis and Bacillus brevis based on PCC analysis. The correlations among the bacteria from the same tissue such as the leaves, sticks and roots were significantly positive, while the correlations among the bacteria from the different tissues were negative. The correlation coefficient of endophytic bacteria between the leaves and the sticks was over 0. 55 (P<0. 05). Based on clustering analysis of 16S rRNA gene sequences, citrus endophytic bacteria was divided into two groups:Gram-positive and Gram-negative. The correlations between HLB bacterium and other bacteria were divided into 3 groups. The bacteria in group I distributed in all leaves; and the bacteria in the group II were negatively corrected to HLB bacterium while in the group III bacteria resided only in certain leaves. When mahalanobis distance was 27. 23, the endophytic bacteria were clustered into three groups. The bacterias in group I distributed in all leaves, so called completely distribution, but the bacteria in group II were incompletely distribution, and the bacteria in group II only distributed in the roots. Based on the community diversity indexes of Shannon, Simpson and Pielou, it is concluded that the maximum of SHANNON(H1 ) index was in the leaves, and the minimum was in the roots, however, the maximum of SIMPSON(D) index was in the sticks, and the minimum was in the roots and the maximum of Pielou index was in the roots while the minimum was in the sticks.