Herein, the deteriorating aspects of a historical manuscript (papers and leather bookbinding) dated back to the 17th century were evaluated with reference to the role of the associated fungal communities. The deterioration signs were investigated using visual assessment, SEM, ATR-FTIR, XRD, color changes, and pH values compared with control. Data showed that the most deterioration aspects were represented by the dust, dirt, erosion, stains, bores, weakness, missed parts, decreasing in paper crystallinity, shifting of wavenumbers of cellulosic band, and changing of color and pH. The dependent-culturable technique showed that thirteen fungal strains were associated with historical manuscript and identified using traditional and molecular methods as Aspergillus niger (three isolates), A. fumigatus (two isolates), A. quadrilineatus (three isolates), Penicillium citrinum (two isolates), and P. chrysogenium (three isolates). These fungal strains showed high efficacy to secretion various hydrolytic enzymes including cellulase, amylase, gelatinase, and pectinase which play a critical role in biodeterioration.