[Background] It was rare to compare the difference of endophytic bacterial communities in apple varieties thought many investigations had been reported on endophytic bacteria in apple trees recently. [Objective] By analyzing and comparing the diversity of endophytic bacterial communities in apple trees of 8 different varieties in Xinjiang and Kyrgyzstan, the abundant microbial resources would be explored. [Methods] Using MiSeq high-throughput sequencing method, sequences at V3?V4 regions of the 16S rRNA gene were amplified, then communities and functions of endophytic bacteria were analyzed in these apple varieties. [Results] valid sequences of 61 487?71 583 bp were obtained from varieties of apple trees, respectively, which clustered into 24?92 distinct operational taxonomic units (OTUs). Shannon index and Simpson index were 0.729?1.177 and 0.265?0.457, respectively. Species diversities of endophytic bacteria in Xinjiang apple varieties were richer than that in Kyrgyzstan varieties. The taxonomic analysis of endophytic bacteria showed that total OTUs of Proteobacteria and Actinobacteria covered 61.16%?97.08% of endophytic bacteria in different apple trees, respectively. They were the dominant bacteria phylum of apple trees. The number, composition and abundance of dominant genus were different in these varieties. OTUs in the genus Massilia and Arthrobacter were the richest, ranging from 6.06%?71.37% and 1.29%?17.86%, respectively. There were some microbial groups of beneficial functional characteristics related to promoting growth, stress resistance or degradation of toxic and harmful substances in the environment in these dominant bacteria. The function prediction showed that the functions of endophytic bacterial community in different apple varieties were different. The function informations of microbial community of Xinjiang varieties were more than that of Kyrgyzstan varieties, which included chemoheterotrophy, aerobic chemoheterotrophy, ureolysis, arsenate detoxification and dissimilatory arsenate reduction. In addition, a large number of unclassified genera were observed in these varieties, ranging from 13.74% to 69.60%. [Conclusion] The diversity of endophytic bacterial communities of these apple varieties were relatively rich, and there were significant differences in the composition and function. Meanwhile, it provided clues to mine new microbial resources and explore the function of endophytic bacterial communities in apple varieties.