Molecular identification of organisms is now a common practice and, increasingly, species are identified from environmental samples. However, for most organisms, we still lack comprehensive reference databases of DNA barcodes to identify the sequences produced. We present a near-complete database of ITS and mtSSU barcodes, named Martin7, for accurate molecular identification of epiphytic lichens (mycobionts) of central Europe. New data were obtained by Sanger and PacBio sequencing. We obtained 907 ITS sequences from 603 species and 844 mtSSU sequences from 546 species and supplemented our dataset with sequences from other reliable sources. In total, 1,172 species are included in the database, 1,004 for the ITS barcode and 906 for mtSSU. ITS was newly sequenced for 224 species and mtSSU for 234 species. For 45 genera these are the first ITS or mtSSU (or both) barcodes ever obtained. In most cases, these barcodes distinguish species as currently circumscribed, but we detected 82 groups or pairs of species where at least one of the barcodes (mostly mtSSU) does not clearly discriminate between species. We revealed diverging genotypes, possibly representing cryptic taxa, within 37 traditionally conceived species. By sequencing phenotypically unidentifiable lichens, we detected numerous “known-unknowns” (presumed undescribed species), especially in the genera Bacidina and Micarea. Five species of sorediate crustose lichens are newly described in the genera Bacidina (two species), Chrysothrix, Japewia and Lecanora. We provide a number of taxonomic novelties, for example that Lecidea betulicola and L. coriacea are teleomorphs of Cheiromycina, and Dictyocatenulata is an anamorph of Thelenella.