The annotated catalogue of lichenized and lichenicolous fungi of Slovenia is based on a comprehensive compilation of literature data. The currently known flora is composed of 860 taxa that includes 787 species of lichenized fungi with 22 varieties, 9 subspecies, 2 forms and 40 lichenicolous fungi (39 species and 1 variety). 30 records remain dubious. 24 non-lichenized species, which are traditionally included in the lichenological literature are mentioned. For each taxon references are listed according to the phytogeographical regions and known substrates are provided. The Alpine phytogeographical region is the part of the country with the highest number of known taxa (602) followed by the Dinaric region (532).