IntroductionThe ecological balance of the plant microbiome, as a barrier against pathogens, is very important for host health.Coptis chinensisis one of the important medicinal plants in China. In recent years, Illumina Miseq high-throughput sequencing technology was frequently used to analyze root rot pathogens and the effects of root rot on rhizosphere microorganisms ofC. chinensis. But the effects of root rot infection on rhizosphere microecological balance ofC. chinensishave received little attention.MethodsIn this study, Illumina Miseq high-throughput sequencing technology was applied to analyze the impact on microbial composition and diversity ofC. chinensisby root rot.ResultsThe results showed that root rot infection had significant impact on bacterial α-diversity in rhizome samples, but had no significant effect on that in leaf samples and rhizosphere soil samples, while root rot infection exhibited significant impact on the fungal α-diversity in leaf samples and rhizosphere soil samples, and no significant impact on that in rhizome samples. PCoA analysis showed that the root rot infection had a greater impact on the fungal community structure in the rhizosphere soil, rhizome, and leaf samples ofC. chinensisthan on the bacterial community structure. Root rot infection destroyed the microecological balance of the original microbiomes in the rhizosphere soil, rhizome, and leaf samples ofC. chinensis, which may also be one of the reasons for the serious root rot ofC. chinensis.DiscussionIn conclusion, our findings suggested that root rot infection withC. chinensisdisrupts microecological balance of rhizosphere soil and endophytic microbiomes. The results of this study can provide theoretical basis for the prevention and control ofC. chinensisroot rot by microecological regulation.