Abstract: Illumina Miseq high-throughput sequencing technology was used to investigate the differences in endophytic fungal and bacterial community structure between healthy and diseased needles of Taxus cuspidata in artificial and natural forests. The results showed that the changes of fungal OTU（Operational Taxonomic Units） were small and the changes of bacterial OTU were large. The natural forest had more fungal OTU number than the artificial forest, and the difference of bacterial OTU number was smaller. There were 9 fungal OTUs in the four groups, accounting for 9.37% of the total fungal OTU. There were 34 identical bacterial OTUs in the four groups of samples, accounting for 4.19% of the total bacterial OTU. At the phylum level, the fungal community composition in the samples before and after infection was basically the same, but degree of relative abundance was significantly different. Compared with the natural forest, the relative abundance of Ascomycota was higher in the artificial forest. Ascomycota was dominant in the four groups of samples. The bacterial community structure and relative abundance changed greatly before and after infection. There were more bacterial species in artificial forests than in natural forests. At the genus level, Genolevuria was the most dominant fungus in healthy leaves of plantations. Dothiora was the most dominant fungus in diseased leaves of plantations, Buckleyzyma was the most dominant fungus in known genera of healthy leaves of natural forests. Genolevuria was the most dominant fungus in the known genera of diseased leaves in natural forests. Ralstonia was the most dominant bacteria in healthy leaves of plantations, 1174-901-12 was the most dominant bacteria in diseased leaves of plantations, Sphingomonas was the most dominant bacteria in known genera of healthy leaves of natural forests. Massilia was the most dominant bacterium in the known genus of natural forest leaf disease. It was speculated that Alternaria and Seimatosporium may cause leaf blight of Taxus cuspidata.