Abstract: This study investigated the community composition and diversity of endophytic fungi in the leaves of "Rabbit-eye" blueberries from Lanping, Dali, and Jingdong in Yunnan Province through Illumina high-throughput sequencing. It also explored the effects of ecological and climatic factors as well as cultivation management practices on the community structure of these fungi and predicted their potential ecological functions based on the FUNGuild database. Results showed that a total of 663 OTUs were detected across all samples, classified into 8 phyla, 31 classes, 89 orders, 187 families, 289 genera, and 389 species. 13 OTUs were shared among all regions, with the number of unique OTUs following the order: Dali > Lanping > Jingdong (P < 0.05). The alpha diversity and richness of the endophytic fungal communities were the highest in Dali and lowest in Jingdong (P < 0.05). At the phylum level, Ascomycota was dominated in Dali (82.13%) and Lanping (88.17%), while the dominant phylum in Jingdong was unclassified fungi (Fungi_phy_Incertae_sedis) (40.92%). At the genus level, Cladosporium (38.99%) and Leptosphaerulina (13.02%) were the dominant genera in Lanping, Epicoccum (20.81%) and Cladosporium (9.66%) in Dali, and unclassified fungi and unknown fungi (unclassified_k__Fungi) accounted for 60.82% of the community in Jingdong. Significant differences in the relative abundance of the top 30 genera were observed among the regions (P < 0.05). Functional prediction using the FUNGuild database revealed that the Pathotroph-Saprotroph-Symbiotroph functional group was predominant in Lanping (44.65%), the unknown nutritional group in Jingdong (61.6%), and the Pathotroph-Saprotroph group in Dali (34.74%). Correlation analysis showed that annual average temperature and plastic film covering cultivation had opposite effects on the relative abundance of dominant genera compared to other environmental factors. These two factors were positively correlated with the relative abundance of five genera, including Trichosporon (P < 0.001), and negatively correlated with six genera, including Cladosporium (P < 0.05). In contrast, 9 genera, including Rhodotorula, were not significantly affected by ecological and climatic factors or cultivation practices, suggesting broader survival adaptability. In conclusion, significant differences in the community composition, diversity, and ecological functions of endophytic fungi in "Rabbit-eye" blueberry leaves were observed across different regions in Yunnan. Ecological and climatic factors and cultivation management practices had distinct impacts on the community structure of these fungi.