•We measure the habitat relationships of wood-inhabiting fungi using DNA metabarcoding.•Old stands had larger species pools, at the landscape but not at the trunk scale.•High landscape-scale forest cover supported trunk scale fungal richness.•Increase in local dead-wood volume increased number of red-listed species per trunk.•Conservation conclusions based on DNA in wood same as in former fruit-body surveys. Understanding the distribution of biodiversity across forest landscapes is a key issue for the spatial planning of conservation management. Obtaining such spatial perspective is challenging because a large part of biodiversity remains hidden to the conventional survey approaches. High-productivity forests are probably the hotspots of hidden biodiversity and, at the same time, under severe timber harvesting pressure. We used DNA-metabarcoding approach to assess habitat quality of successional high productivity forests for wood-inhabiting fungi, focusing on fungal diversity that remains hidden in fruit-body surveys. We sampled a fixed amount of coarse fallen Norway spruce trunks in 40 naturally developing stands ranging from 44 to 140 years of age in hemi-boreal Estonia. We found three main habitat quality patterns. The total number of fungal OTUs in older (>80 years) stands exceeded that in younger stands due to the accumulation of rare fungi. The proportion of trunks hosting highest number of OTUs and trunk-scale richness of rare fungi were greatest in stands surrounded by extensive forest area. The average number of red-listed species per trunk increased mainly along with the volume of fallen dead wood; large volumes provided quality habitats already before the stands had reached 80 years of age. These results support the view that both substrate amount in the forest stand and habitat connectivity on a landscape scale support fungal diversity in dead wood. Earlier studies on wood-inhabiting fungi have reached similar conclusions based on observations of fungal fruit-bodies. Thus, the overall principle of focusing conservation efforts to remaining high quality habitats and landscapes extends to the fungi hidden to the conventional survey methods.