Abstract: 【Objective】The aim was to compare the characteristics and functional differences of the endophytic bacterial communities in the stem tissues of healthy and canker diseased pitaya plants, so as to provide theoretical basis for revealing the occurrence mechanism of pitaya canker and studying the prevention and comprehensive control techniques.【Method】Stem tissues of healthy and canker diseased pitaya plants were collected, and the 16S rDNA sequences of endophytic bacteria in the stem tissues were determined using Illumina Miseq sequencing platform to analyze the differences of bacterial community characteristics in the stems of healthy and diseased plants. 【Result】The bacterial community species and amplicon sequence variants(ASVs) in the stems of healthy pitaya plants were lower than those of diseased plants, there was no significant difference in bacterial community diversity between healthy plants and diseased plants(P>0.05).Among the bacterial dominant bacterial phyla, the relative abundances of Actinobacteriota, Chloroflexi and Deinococcota in the stem tissue of diseased plants were higher, while the relative abundance of Bacteroidota in the stem tissue of healthy plants was higher. There were 27 dominant bacterial genera in the stem tissue of diseased plants, and the relative abundance of Pseudomonas, Bacillus, Sphingomonas, Deinococcus, Clostridium_sensu_stricto_1, Curtobacterium, Xanthomonas, Lachnoclostridium, Microvirga, Lysobacter, Klenkia and Paenibacillus was higher. There were 26 dominant bacterial genera in the stem tissue of healthy plants, and the relative abundance of norank_f_Muribaculaceae, Bacteroides, Lactobacillus, Methylobacterium-Methylorubrum, unclassified_f_Xanthomonadaceae, Parabacteroides, Ralstonia, Rhodococcus, Streptomyces, Bifidobacterium, Acinetobacter and Cellvibrio was higher. The results of linear discriminant analysis(LEfSe) showed that there were more indicator bacteria in the stem tissue of healthy plants than those in the stem tissue of diseased plants, while the indicator bacteria in the stems of diseased plants only belonged to four different genera, namely Xanthomonas, Curtobacterium, Lachnochlorostridium and Novosphingobium. The results of bacterial function prediction showed that the gene copy numbers of endophytic bacteria in the four secondary functional layers of membrane transport, carbohydrate metabolism, other amino acid metabolism and other secondary metabolite biosynthesis were significantly higher than those in healthy plant stems(P<0.05). 【Conclusion】After the occurrence of pitaya stem canker, there is no obvious change in the diversity of the endophytic bacterial community in the stem tissues. However, the proportions of some dominant bacterial phyla and genera change obviously. Among them, four indicator bacterial genera may be related to the occurrence of stem ulcer disease.