Abstract: Aims Pinus squamata, is a critically endangered species endemic to China, found only in Qiaojia County, Yunnan Province. It faces significant challenges such as fragile habitats and difficulties in population recovery. Fungal communities play a vital role in the population maintenance and ecological adaptation of endangered plants. However, studies on the fungal community characteristics within the roots and rhizosphere of P. squamata are currently insufficient. Methods This study used in-situ sampling and high-throughput sequencing to analyze the fungal community structures and geographical differentiation patterns of wild and cultivated populations of P. squamata. Additionally, it compared the fungal community structures of Pinus squamata with those of its neighboring plant species. Important findings (1) There are significant differences in the fungal community structures within the roots and rhizosphere between the wild and cultivated populations of P. squamata. The fungal diversity in the wild populations is lower than that of the cultivated population. (2) In the wild populations, the fungal communities differ significantly between individuals in the west-slope and east-slope populations. (3) Ectomycorrhizal (ECM) fungi, such as species from the genera Sebacina, Russula, and Xanthoconium, dominate the root systems of Pinus squamata. Individuals in the west-slope population, which inhabit nutrient-poor soils, exhibit greater dependence on ECM fungi. (4) P. squamata shares some ECM fungi with neighboring tree species, highlighting the cooperative role of mycorrhizal fungal networks in resource sharing and ecological stability. This study reveals both abiotic and biotic factors influencing the fungal communities of P. squamata. Results of this study suggest that conservation efforts should combine inoculation with ectomycorrhizal fungi and improvement of the seedling soil to restore critical ectomycorrhizal networks, thereby promoting the vision of integrated recovery of the “pine-fungus” system.

Key words: Endangered plants, extremely small population, Pinus squamata, Ectomycorrhizal fungi, Root-associated fungal community, Conservation strategies