Austria – albeit a small country – is especially rich in ecosystem and habitat types with influences from Atlantic, alpine, submediterranean and continental climates. Elevation ranges from ca. 120 m to nearly 3800 m. Many habitat types are, however, threatened due to climate change and human activities like agriculture, forestry, infrastructure work or tourism. Decline and loss of plant and animal species due to these changes is well documented, whereas less is known from fungal species. A comprehensive survey of soil fungal communities was carried out in semi-natural and near-natural ecosystems throughout Austria, from riparian forests in the Pannonian lowlands to alpine scrub and pastures. Samples were collected in ICP forest sites, LTER sites, national parks and natural forest reserves with well documented data on site characteristics, vegetation, soil properties, climate, disturbance history etc. From many sites, archived samples in soil libraries are available. Although archives were established for physicochemical analyses, initial experiments indicated that long-term stored soil samples are as well suited for DNA-based fungal community analyses. It is thus possible to compare soil fungal communities from the early 1990ies until the present for improved prediction of future developments. Dynamics in fungal community composition across space and time and data on major drivers of changes will be presented. Currently available data highlight the importance of habitat conservation for protection of a high fungal biodiversity across different ecosystems.