Abstract: 【Objective】To analyze the community structure and diversity of endophytic bacteria in banana roots of resistant and susceptible banana varieties and explore the association between resistance to fusarium wilt and the root microbiome of banana，which would provide theoretical basis for exploiting and utilizing indigenous biocontrol microbiome of banana fusarium wilt. 【Method】The banana fusarium wilt susceptible variety Williams B6 and resistant variety Zhongjiao 9 were used as materials. The banana root system was collected at the initial stage of fusarium wilt（the period of vigorous vegetative growth）and the severe stage（the period of gestational bud stage），the incidence of banana was investigated before two sampling；the root DNAof susceptible and disease-resistant banana plants was extracted respectively. The V3-V4 region of 16S rRNAgene of endophytic bacteria in banana roots was sequenced by high-throughput sequencing technology. Raw sequencing files were quality-filtered by Fastp and merged by Flash. The taxonomy of each 16S rRNA gene sequence was compared and annotated by RDP classifier algorithm against the Silva 16S rRNA database. Excel 2010 was used to analyze the data，and DPS 7.0 software was used for significant difference analysis.【Result】With the growth and development of banana，the fusarium wilt became more and more serious，and the resistant variety Zhongjiao 9 showed extremely significant（P<0.01）disease resistance compared with the susceptible variety Williams B6 during the growth process. A total of 2568 OTUs were obtained by high-throughput sequencing，which belonged to 1139 species， 673 genera，369 families，220 orders，89 classes，and 32 phyla. The results of Alpha diversity and species composition analysis showed that the root bacteria diversity of resistant variety Zhongjiao 9 was higher than that of susceptible variety Williams B6，but the differences was not significant（P>0.05）. There was no difference in the dominant bacterial phyla of root bacterial community between the two varieties at the initial stage and the severe stage，however，the relative abundances changed significantly with the growth of bananas（P<0.05，the same below）. At the initial stage，the main dominant bacterial genus in the root system of susceptible and disease-resistant bananas was relatively single，while the bacterial community composition in the severe stage was more abundant，the relative adundance of beneficial microorganism Streptomyces，Bacteroides and Brevibacterium increased significantly in the resistant banana variety，genus Brevibacterium was found and enriched only in the roots of resistant variety. NMDS and PCoA analysis showed that the community structure of endophytic bacteria in the disease initial stage was basiclly the same，and the community structure of endophytic bacteria of disease-resistant variety in the severe disease stage was significantly different from the other treatment group.【Conclusion】The community structure of endophytic bacteria in the root of susceptible and disease-resistant banana changes with the progression of the disease process. The community composition of dominant phyla and genera vary significantly，especially the relative abundance of beneficial microorganism increas significantly in resistant variety. The variation of root microbial structure of susceptible and resistant banana have great effect on the occurrence of fusarium wilt，and the accumulation of specific microorganisms has direct or indirect effect on fusarium wilt resistance of banana.