Seedling root rot is widespread and devastating to naked barley,yet the differences of fungal community in rhizosphere soil across differing disease incidences remain unclear,hindering the development of specific and effective control strategies. To clarify these dynamics,rhizosphere soil samples from healthy (MH) and seedling naked barley affected by root rot with incidences of 5% (MD1),10% (MD2),15% (MD3),and 20% (MD4) were selected for DNA extraction,with the 18S rDNA region amplified and subjected to high-throughput sequencing via Illumina-Miseq. These sequences were classified taxonomically,annotated,and analyzed to identify differences in fungal community diversity,composition,and structure. The OTU classification outcomes indicated that MD2 harbored the greatest number of OTUs and unique OTUs,whereas MD1 contained the fewest. The shared OTUs between MH and MD1,MD1 and MD4 were minimal,contrasted with the abundant shared OTUs between MH and MD3. Observed species,PD whole tree,and Chao1 indices of MD2 were significantly the highest among the samples. Examining fungal community structure and composition at various taxonomic levels,along with LEfSe (Linear Discriminant Analysis Effect Size) analysis,showed that the relative abundance of dominant phyla,such as Ascomycota and Basidiomycota,displayed opposing trends with escalating disease incidence,with notable enrichment in MD1 and MD3,respectively. The dominant class Sordariomycetes was enriched in MH and its abundance waned post-infection. Classes such as Dothideomycetes,Leotiomycetes,and Pezizomycetes were enriched in MD1. Glomerales showed peak abundance in MD2 and a nadir in MD3. In diseased samples,the relative abundance of dominant families like Pezizaceae,Tricholomataceae,Ascobolaceae,and Phaeosphaeriaceae generally inversely changed with the changing incidence. The abundance of Pezizaceae significantly declined,but other families with variable increases. Correlation clustering and PCA analysis indicated that the fungal diversity and community structures of MD3 and MD4 were similar,as were those of MD1 and MD2 to a greater extent. These insights imply that during the spread of seedling root rot,pathogenic fungi impede the enrichment of other microbial communities,diminishing fungal species diversity and disrupting the equilibrium of beneficial interactions among microorganisms. Moreover,the prevalent pathogenic groups vary with different incidences,and the functional impact of the same microbial community differs across naked barley fields. The incipient phase of root rot (5%-10% incidence) may stimulate rhizosphere defense of fungi and promote beneficial microbial enrichment to sustain soil ecological stability. However,the capacity for self-stabilization of rhizosphere soil fungal community is limited,allowing pathogenic fungi to dominate,beneficial fungal communities are suppressed,and fungal community species diversity decreases in the later prevalence of the disease (15%-20% incidence).