Keraton Kasepuhan Cirebon has collection of five old manuscripts of European origin from 19th century, and the former library of Faculty of Humanities Universitas Indonesia has collection of four old manuscripts of European paper origin from 19-20th centuries. The objectives of this study were to isolate and morphologically characterize fungi from nine old manuscripts of European origin. All manuscripts showed brown and black spots, and fungal spores on the surfaces. Observation by loop was carried out in the field to determine the type of paper and to detect biodeterioration of the manuscripts. Twenty-two fungal isolates were obtained by sterile cotton swab and the culture-dependent method on Dichloran Glycerol Agar (DG18). Detection of fungal deterioration on paper was investigated by using paper strip method with old paper of European origin on Czapek's Dox Agar (CDA) without carbon source. The paper strips were inoculated with cell suspension at a concentration of approximately 1 × 107 cell/mL. Twenty fungal isolates were able to grow on the old paper strips indicating that the old manuscripts are liable to fungal degradation. The fungal isolates were xerophilic in nature. Morphological characterization described the fungal isolates in the genera of Aspergillus, Penicillium, and Eurotium. Three fungal isolates could not be described and were grouped as Mycelia sterilia. Basic local alignment search tool (BLAST)-based identification and phylogeny-based identification using the data set of internal transcribed spacer (ITS) sequences is required to determine the species identities of the fungal strains.