Abstract: Huanglongbing (HLB, a yellow shoot disease) is the most destructive citrus disease in the world. Plant endophyte communities of red pomelo have been associated with HLB. It was therefore important to investigate the endophyte community of red pomelo plant in relation to HLB. In this paper, endophyte community structures in different spatial positions and healthy conditions of HLB-affected red pomelo plants were analyzed using phospholipid fatty acids PLFAs biomarkers based at Sherlock MIS (MIDI Inc.). Based on the results, 42 PLFAs were detected and 9 of them had wild distributions across all the samples while the other 33 were mainly distributed in different leaf orientations. Cluster analysis showed that PLFAs in different leaves in space existed into two community groups. While PLFAs in the group I belonged to an incomplete distribution, PLFAs in group Ⅱ were distributed almost in all samples. There existed some differences in PLFAs content and composition in leaves of HLB-affected red pomelo plants in different spatial positions and health conditions. When compared among each other, it was noted that PLFAs content in east-oriented leaves were maximum among different orientations. The same was true for lower parts leaf in PLFAs content. Healthy leaves contain more PLFAs than HLB-affected leaves. Furthermore, south-oriented leaves had the highest fungi/bacteria PLFAs ratio and also higher G⁺/G^- (gram-positive bacteria/gram-negative bacteria) PLFAs ratio than north/west-oriented leaves. There was no significant difference in fungi-to-bacteria PLFAs ratio at different leaf levels. However, significant differences existed in PLFAs G⁺/G^- ratio in different height leaves. While the highest ratio occurred in the leaves at the upper parts of plant, the lowest ratio was in leaves at the middle parts of plant. Fungi-to-bacteria PLFAs ratio was higher in healthy leaves than that in HLB-affected leaves. Diversity indexes of Shannon, Simpson and Pielou of endophyte communities among leaves with different orientations and healthy conditions were significantly different. However, no apparent differences were noted among different heights leaves. Principal component analysis showed that the first and second principal components accounted for a total of 82.99% of the variation, which may distinguish endophyte communities in leaves with different orientations. Cluster analysis divided healthy leaves in two groups, and HLB-affected leaves in the other group. The results indicated that the distribution of PLFAs was related with health conditions and orientations of leaves, and was more closely in the former than the latter.