This study evaluates the effectiveness of Illumina-based genome skimming for barcoding myxomycete herbarium collections ranging from 29 to 91 years in age. Despite significant DNA fragmentation, we successfully recovered partial sequences of the standard barcode marker (nucSSU) in all cases. For some collections, additional markers were recovered, including EF1a, COI, and mtSSU, contributing to a total of 28 recognized genes. In a 33-year-old specimen of Lindbladia tubulina, the assembly reached an N50 of 4.19 kb, enabling the recovery of extended functional loci. It was found that within the 29–91-year timeframe, specimen age does not strictly correlate with genomic informativeness, thus allowing us to conclude that even older collections can be successfully barcoded. The input genomic DNA quantity emerges as the primary determinant of sequencing success. Samples with high DNA yields provide representative amounts of contigs coming certainly (matching sequences in the NCBI nucleotide database) or presumably (no matches) from myxomycetes, regardless of specimen age. The taxonomic interpretation of the non-target fraction of contigs revealed distinct signals of both anthropogenic contamination (human DNA and skin microflora) and natural substrate inhabitants, including oribatid mites and bacteria from dead wood, soil, and grass litter. The results demonstrate that short-read genome skimming can provide a bridge to integrate historical type material of myxomycetes into contemporary phylogenetic research. This method can effectively overcome the length-dependent limitations of traditional Sanger sequencing, thus providing a roadmap for the future of museomics in myxomycetology.