Fungi are irreplaceable symbionts, drivers of ecological balance, and decomposers that enable the cycling of matter and energy. The biodiversity of fungi is measured in millions of species, but less than 10% of their total number is known to science. The Dinaric Karst is one of the most important karst regions in the world in terms of biodiversity and hydrology, where fungi are poorly studied. This area is particularly important for the preservation of drinking water resources, the quality of which is significantly influenced by the organisms living there. Permanent darkness, high humidity, and steady temperature make caves natural laboratories in which fungi are exposed to selection pressures that lead to diverse adaptation mechanisms. Therefore, we assume that these fungi have exceptional bioindicator and bioprospecting potential. This is the first systematic study of fungi in the Dinaric Karst involving interdisciplinary research in the scope: cave ecosystem - total fungal biodiversity - fungal organisms - bioindicators - secondary metabolite profiling - biological potential. The objectives of the project are to explore the biodiversity of cave fungi and to ascertain their ecological and biogeographical characteristics. In addition, the biological activity of their extracts will be tested for the selected fungal species, a profile of secondary metabolites will be established, and chemical characterisation of the potentially bioactive compounds will be carried out. The research will be conducted in hydrologically active cave systems in Croatia and Bosnia and Herzegovina, in Mediterranean, Alpine, and Continental ecoregions, in five different geo-tectonic units and all ecological niches. The expected results will make an important contribution to the knowledge of biodiversity and ecological relationships in the karst underground and give insight into the bioactive potential of cave fungi, with the aim of providing guidelines for future biotechnological research.