With the advent of high-throughput sequencing techniques, natural history museums and herbaria have become new frontiers for genetic research. Genomic information from historical specimens has provided evidence to solve significant questions in broad research areas. However, access to such valuable genetic resources remains limited in lichens due to experimental challenges in extracting and amplifying highly degraded DNA in historical specimens. So far, only a handful of studies have reported successful sequencing of several short genetic markers from historical lichen specimens despite the increasing importance of genetic information in lichenology. Here, we aimed to establish an efficient method for sequencing the whole genome of historical lichen specimens. We modified a method used in ancient DNA studies and sequenced the whole genome of Usnea and Cladonia specimens, including lectotype and holotype. Our approach shows that 2.7%–23.3% and 3.0%–11.8% of the total sequenced reads originate from the genomes of fungal (mycobiont) and algal (photobiont) symbionts, respectively. The mycobiont- and photobiont-derived reads are comprised of DNA fragments shorter than 46 bp, covering 73%–99% and 92%–99% of the mycobiont and photobiont reference genomes, respectively. We retrieved 792,245 and 410,705 Single Nucleotide Variant sites (SNVs) to perform phylogenetic analysis of the U. hakonensis and C. kurogawae mycobionts, respectively. We also demonstrated experimental modifications that improved proportions of symbiont-derived reads within sequenced data. We believe that our method is applicable to lichen specimens in a broad range of ages and taxonomic groups, thereby potentially converting historical lichen specimens into resources of genome-wide studies. Keywords: genome sequencing | historical specimens | lichen | type specimens.