Background: The experimental materials were a 60-year-old tea tree (cv. Shu Cha Zao; SCZ) (the mother plant), and 1-year-old and 20-year old plants of SCZ that originated as cuttings from the mother plant. The aim of this study was to explore the spatial and dynamic distribution of endophytic fungi in different leaf niches (upper leaves, middle leaves, lower leaves) and rhizosphere soil on tea plants (Camellia sinensis) which with different ages in the same garden by high-throughput sequencing.Results: In this study, Ascomycota (83.77%), Basidiomycota (11.71%), and Zygomycota (3.45%) were the three dominant fungal phyla in all samples. Cladosporium (12.73%), Zymoseptoria (9.18%), and Strelitziana (13.11%) were the dominant genera in the leaf. Alpha diversity analysis revealed that endophytic communities in leaves differed from those in rhizosphere soil and different leaf niches had similar fungal diversity. Shannon’s indices and NMDS analysis indicated significant differences in fungal diversity and composition among the SCZ trees of different ages (p≤0.01). The abundance of Cladosporium and Zymoseptoria decreased with increasing SCZ age, whereas the abundance of Strelitziana increased.Conclusions: Our results illustrate the variation in endophytic fungi among different niches on tea plants of different ages. The distribution of endophytic fungi in leaves of C. Sinensis (cv. Shu Cha Zao) has a certain spatiotemporal variation.