Dead wood constitutes an important substrate for biodiversity in boreal forests. Changes in forest age structure and availability of dead wood trough management are affecting lichen species density, especially for red-listed species. To study the effects of natural wood decay on lichen communities we investigated 230 snags of Picea abies, displaying different stages of decomposition. Sampling was performed at two different elevations (800–900 and 1000–1100 m a.s.l.) in the national park “Bayerischer Wald” at the German-Czech border. The site is a mixed deciduous and coniferous montane forest which undergoes natural forest dynamics and therefore harbours large amounts of standing dead wood. Decay stages of the wood, light availability, elevation, years since the death of the tree and bark coverage was documented. We recorded more than 3200 specimens comprising more than 160 species. The lichen diversity and community assembly patterns were explored through non-metric multidimensional scaling. Our findings suggest that the degree of wood degradation is a highly important factor determining species richness and community composition. Several rare or endangered species are dependent on different stages of decay, highlighting the importance of maintaining a diversity of available substrates.