BACKGROUND/AIMS: The European larch is a pioneer tree and a valuable economic resource in subalpine ecosystems, thus playing crucial roles to ecosystem services and human activities. However, their ectomycorrhizal fungal community remains unknown in high altitudinal natural habitats. Here, we explore the mycobiont diversity of METHODS: Our approach combines morphotyping of mycorrhized root tips with molecular analysis. Particular effort was given to monitor both ectomycorrhizal host-specialist and -generalist fungi. RESULTS: Both adult and young trees show a 100% mycorrhization rate, with a total diversity of 68 ectomycorrhizal species. The ectomycorrhizal composition is dominated by typical host specialists of larch trees (e.g., CONCLUSIONS: This study suggests potential mycobiont community shifts across climatic conditions with significant implications for the adaptability and resilience of subalpine forests in the face of climate change. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11104-024-06721-8.