[Objective] To explore the diversity and community compositions of onshore soil and plant endophytic fungi in the soil zones at different exposure periods and their response to continuous lake desiccation in the Aral Sea. [Methods] Soil samples were collected from farshore (exposed before 1970) towards the present shoreline in the Aral Sea, followed by geochemistry and mineralogy analysis. At the same time, soil samples and dominant aboveground plants from different onshore soil zones were collected, and their fungal diversity were analyzed by ITS gene high-throughput sequencing. The fungal response to lake desiccation (such as salinity, mineralogy and plant species) were explored. [Results] The results showed that the continuously exposed lake bed formed an increasing gradient of total soluble salts:E48 (exposed before 1970, total soluble salts (in abbr. TSS):0.5±0.5 g/L);E38 (exposed before 1980, TSS:0.4±0.2 g/L);E28 (exposed before 1990, TSS:23.3±2.1 g/L);E18 (exposed before 2000, TSS:23.7±7.5 g/L);E9 (exposed before 2009, TSS:71.3±6.1 g/L);E1 (exposed in 2017, TSS:62.9±10.7 g/L); E0 (the present shoreline in 2018, TSS:69.9±8.3 g/L). These soil zones were inhabited by different plants:Haloxylon ammodendron were dominated in the E38 and E28 zones; Chenopodium album were dominated in the E28, E19 and E9 zones; and no visible plants were found in the E1 and E0 zones. In addition, the mineralogical composition varied among different soil zones:the contents of clay mineral and evaporites generally increased from farshore towards the present shoreline of the Aral Sea, while the content of carbonates gradually decreased. The dominant fungal communities (>5%) in the studied soil samples were Eurotiomycetes, Sordariomycetes, Leotiomycetes, Dothideomycetes, Ustilaginomycotina and Agaricomycetes, and were clustered by plant species richness. While a large number of unknown fugal species (>97.8%) were dominated in the endophytic fungal communities, and were clustered by plant species. Linear regression showed that the fungal community differences in the soil sample from different onshore soil zones had a significant (R²=0.32, P<0.05) correlation with the exposure time difference, whereas there was no significant correlation with the difference in total soluble salts. In addition, there was no significant difference between the plant endophytic fungal community difference and exposure time distance and total soluble salts difference. Mantel test showed that fungal communities in different soil zones had significant (P<0.05) correlations with plant species richness and dolomite, calcite, microcline and gypsum. Among them, plant species richness and calcite were the most important factors influencing on soil fungal communities. There was a significant (P<0.05) correlation between the plant endophytic fungal community and calcite. [Conclusion] The community compositions of soil fungi and plant endophytic fungi in different Aral Sea soil zones show temporal and spatial variations, which could be ascribed to plant species (richness) and specific mineral compositions, but not significantly correlated with total soluble salts.