Abstract: 【Objective】 This study aimed to investigate the effects of different infection degrees of leaf spot disease on structure and diversity of the phyllosphere microbial communities in Gentiana crassicaulis， providing a theoretical basis for disease control and high-quality cultivation for Gentiana crassicaulis.【Method】 Leaves of Gentiana crassicaulis with varying infection degrees （healthy， mild， and severe） were used as experimental materials. High-throughput sequencing was employed to explore the structures of epiphytic and endophytic microbial communities. Alpha and beta diversity analyses were performed and functional predictions for fungal and bacterial communities were conducted.【Result】 Alpha diversity analysis revealed that the Shannon， Chao1， and ACE indexes of epiphytic fungal communities in mildly and severely infected plants were significantly higher than those in healthy plants （P<0.05， the same below）， while the Simpson index was significantly lower. For the epiphytic bacterial communities， the Shannon， Chao1， and ACE indexes of severely infected plants were significantly higher than those of healthy and mildly infected plants. As disease got severer， the Shannon index of the endophytic fungal community showed a trend of first increasing and then decreasing， while the Simpson index showed the opposite. For the endophytic bacterial community， the Shannon index exhibited an increasing trend. However， the Chao1 and ACE indexes of both endophytic fungal and bacterial communities showed no significant differences among different infection degrees （P>0.05）. Beta diversity analysis indicated significant differences between epiphytic and endophytic fungal community structures. Compared with healthy plants， the relative abundances of the pathogenic fungi Septoria and Blumeria increased in both epiphytic and endophytic fungal communities of mildly and severely infected plants. The relative abundance of beneficial bacteria such as Bacillus and Methylobacterium-Methylorubrum increased in the epiphytic bacterial communities. Functional prediction showed that the primary nutritional modes of phyllosphere fungi were saprotrophs， pathotrophs， and symbiotrophs. The proportion of saprotrophs in both epiphytic and endophytic fungal communities of mildly and severely infected plants increased more than that in healthy plants. The main functional groups of phyllosphere bacteria included aerobic chemoheterotrophy， anaerobic chemoheterotrophy， and photoautotrophy. As disease got severer， the proportions of anaerobic chemoheterotrophs and photoautotrophy decreased in the epiphytic bacterial community.【Conclusion】 Different degrees of leaf spot affect the diversity of phyllosphere microbial communities in Gentiana crassicaulis. After infection， the diversity and richness of the epiphytic microbial community increase， while the endophytic microbial community demonstrates greater stability. Different degrees of leaf spot influence both the composition and function of phyllosphere microbial communities.