•Historical disturbances shaped the contemporary local and regional richness of fungi.•Natural disturbances had contrasting effects on fungi at different spatial scales.•Local red-listed species diversity increased due to higher disturbance frequency.•Regional diversity of all species was decreased by higher disturbance severity. Understanding the processes shaping the composition of assemblages at multiple spatial scales in response to disturbance events is crucial for preventing ongoing biodiversity loss and for improving current forest management policies aimed at mitigating climate change and enhancing forest resilience. Deadwood-inhabiting fungi represent an essential component of forest ecosystems through their association with deadwood decomposition and the cycling of nutrients and carbon. Although we have sufficient evidence for the fundamental role of deadwood availability and variability of decay stages for fungal species diversity, the influence of long-term natural disturbance regimes as the main driver of deadwood quantity and quality has not been sufficiently documented. We used a dendroecological approach to analyse the effect of 250-years of historical natural disturbance and structural habitat elements on local (plot-level) and regional (stand-level) species richness of deadwood-inhabiting fungi. We used data collected from 51 study plots within nine best-preserved primary spruce forest stands distributed across the Western Carpathian Mountains. Historical disturbances shaped the contemporary local and regional species richness of fungi, with contrasting impacts of disturbance regime components at different spatial scales. While local diversity of red-listed species has increased due to higher disturbance frequency, regional diversity of all species has decreased due to higher severity historical disturbances. The volume of deadwood positively influenced the species richness of deadwood-inhabiting fungi while canopy openness had a negative impact. The high number of observed rare species highlights the important role of primary forests for biodiversity conservation. From a landscape perspective, we can conclude that the distribution of species from the regional species pool is - at least to some extent - driven by past spatiotemporal patterns of disturbance events. Natural disturbances occurring at higher frequencies that create a mosaic forest structure are necessary for fungal species - especially for rare and endangered taxa. Thus, both the protection of intact forest landscapes and forest management practises that emulate natural disturbance processes are recommended to support habitats of diverse fungal communities and their associated ecosystem functions.