The aim of this study was to identify habitat preferences of red-listed epiphytic and epixylic bryophyte, lichenized and non-lichenized fungi species in woodland key habitats (WKHS) (areas less than 10 ha, where forest structures indicate occurrence of red-listed species) in southern Sweden. The relative importance of different groups of environmental factors was assessed with partial canonical correspondence analysis techniques and a cross-validation approach using data from 7196 selected WKHs. Different woody substrates (old trees, logs and snags) made up the most important variable group for occurrence of red-listed species (30% unique explainable variation). Species associated with Fagus sylvatica and Picea abies habitats, but also species associated with Quercus spp. and Populus tremula habitats showed distinct habitat preferences. The second most important variable group (16% unique explainable variation) was geographical location. A west-east gradient was identified, and species concentrated to Baltic islands in the east were separated from other species. This gradient, and an identified south-north gradient, probably reflect differences in temperatures and rainfall between different regions. Among the remaining variable groups, historical land-use, ground conditions and forest stand composition were of similar importance (5-7% unique explainable variation). Traditional management regimes resulting in semi-open forest habitats (leaf harvesting, forest grazing and selective cutting) were associated with the occurrence of many species, probably due to differences in microclimate between sites of different openness. Furthermore, a ground moisture gradient extending from species associated with dry sites (mainly lichenized fungi) to species associated with wet sites (mainly bryophytes), and a nutrient gradient from species associated with nutrient-poor sites to species occurring at nutrient-rich sites, were identified. Thus, conservation measures are needed in a broad spectrum of habitats with different substrates. Also sites with similar substrates, but situated in different regions (and climates), or with different ground moisture and nutrient conditions are needed to cover the full spectrum of habitat conditions suitable for different red-listed bryophytes and fungi.