Fungal frequency and diversity were studied in historical, parchment and paper documents using Illumina sequencing. In total, 156 494, 52 451 and 41 615 sequences were obtained from three samples. Documents were colonized by 225 taxa. Glomeromycota, Zygomycota, Ascomycota and Basidiomycota were represented by 1, 8, 131 and 83 taxa, respectively. Fungal communities included plant pathogens, epiphytes or endophytes of a wide range of plants and possibly opportunistic plant pathogens, saprotrophs common in soil, on decaying leaves, needles, wood and on other plant material, human pathogens, animal and nematode pathogens, entomopathogenic taxa, mycoparasites, white and black yeast-like taxa, taxa with antagonistic and medicinal properties, lichenized fungi, food contaminants, common contaminants of indoor, built environments, taxa on herbivore dung, keratin-degrading taxa, xerophilic taxa, and an endangered fungi included in the Red List of Threatened Species. A non-destructive and non-invasive method for quantitative characterization of parchment deterioration, based on spectral measurements, was used for evaluating the scale of damage.The collagen-to-gelatin ratio, estimated from the synchronous fluorescence spectra of the studied samples and of pure collagen and gelatin, was suggested for characterizing parchment condition. Analysis of fluorescence peaks indicated the moderate stage of deterioration of the studied documents.