Due to their cryptic lifestyle, hidden diversity and a lack of ecological knowledge, conservation of wood-inhabiting fungi continues to be a niche interest. Molecular methods are able to provide deeper insights into the ecology of rare fungal species. We investigated the occurrence of the rare wood-inhabiting fungus Phellinidium pouzarii across the Bavarian Forest National Park in Germany using a fruit body survey, amplicon sequencing and qPCR. Additionally, we sequenced the genome of P. pouzarii and characterized the chemical substances responsible for its distinctive scent. Our approach gave matching results between amplicon sequencing and qPCRs, however, we found no evidence that P. pouzarii is more abundant in the National Park than we can assume based on fruit body inventories, underlining the species' critically endangered status. Genomics revealed P. pouzarii's repertoire of ligninolytic enzymes, pointing towards a white rot lifestyle. Two main components of P. pouzarii's distinct odour we identified (2-phenylethanol, methyl p-anisate) are known to act as insect attractants and/or to possess antimicrobial properties.