Current trends emphasize the importance of the examination of the functional composition of lichens, which may provide information on the species realized niche diversity and community assembly processes, thus enabling one to understand the specific adaptations of lichens and their interaction with the environment. We analyzed the distribution and specialization of diverse morphological, anatomical and chemical (lichen secondary metabolites) traits in lichen communities in a close-to-natural forest of lowland Europe. We considered these traits in relation to three levels of forest ecosystem organization: forest communities, phorophyte species and substrates, in order to recognize the specialization of functional traits to different levels of the forest complexity. Traits related to the sexual reproduction of mycobionts (i.e., ascomata types: lecanoroid apothecia, lecideoid apothecia, arthonioid apothecia, lirellate apothecia, stalked apothecia and perithecia) and asexual reproduction of mycobionts (pycnidia, hyphophores and sporodochia) demonstrated the highest specialization to type of substrate, tree species and forest community. Thallus type (foliose, fruticose, crustose and leprose thalli), ascospore dark pigmentation and asexual reproduction by lichenized diaspores (soredia and isidia) revealed the lowest specialization to tree species and substrate, as well as to forest community. Results indicate that lichen functional trait assemblage distribution should not only be considered at the level of differences in the internal structure of the analyzed forest communities (e.g., higher number of diverse substrates or tree species) but also studied in relation to specific habitat conditions (insolation, moisture, temperature, eutrophication) that are characteristic of a particular forest community. Our work contributes to the understanding of the role of the forest structure in shaping lichen functional trait composition, as well as enhancing our knowledge on community assembly rules of lichen species.