The purpose of this study is to explore the microbiological mechanism of the root rot of Lycium barbarum Ningqi-7 based on the analysis of microbial composition on rhizoplane and pathogenic microbes. High-throughput sequencing was used to analyze the microbial community composition and diversity. The root rot fungi were isolated with the tissue separation method. The combination of morphology and molecular characteristics was used to identify the fungi. The pathogenicity was identified according to Koch’s rule. The structure of fungal community on the rhizoplane of the diseased plant had been seriously imbalanced, with the richness and diversity being significantly lower than those of the healthy plants. The dominant groups of rhizoplane microorganisms were also quite different between the root rot diseased plants and the healthy plants. The dominant genera on the rhizoplane of the diseased plants were Fusarium and Clonostachys, with relative abundance being 38.81% and 31.24%, respectively ；while the dominant genera on the rhizoplane of the healthy plants were Mortierella（14.09%）and Fusarium（10.38%）. The abundance of potential pathogens on the rhizoplane of the diseased plants was significantly higher than that of the healthy plants. Total 33 fungi were isolated from the root rot of the diseased plants, and they were classified into four genera ：Fusarium, Penicillium, Earliella, and Clonostachys, among which, the highest frequency of isolation was Fusarium, reaching 75.76%. Two species of Fusarium, F. solani and F. oxysporum, caused the root rot of Lycium barbarum Ningqi-7. This study clarified that the occurrence of root rot of L. barbarum Ningqi-7 was not only closely related to pathogenic fungi, but also related to the community structure of rhizoplane microorganisms. [ABSTRACT FROM AUTHOR]