Central Library Universitas Indonesia has a collection of old Chinese manuscripts predicted from 18th-19th century. The collected manuscripts showed signs of deterioration by microorganisms. The objectives of this study were to characterize morphologically and microscopically the isolated filamentous fungi from two deteriorated old Chinese manuscripts from plot 1 Ruang Naskah Central Library Universitas Indonesia. Observation by stereo microscope was carried out to examine the biodeterioration of the old Chinese manuscripts. Sterile cotton swab was used to obtain samples and culture dependent method was used to isolate fungi. The old manuscripts showed signs of deterioration, i.e., brown and black spots on the manuscripts, and the presence of fungal spores. Five fungal isolates were obtained based on the morphological type differences. Based on morphological characteristics, the isolates were identified to the genus level as Aspergillus (2 isolates), Cladosporium (1 isolate), and Penicillium (2 isolates), and they were anamorphic fungi. The results of this study showed that the old Chinese manuscripts were deteriorated by filamentous fungi. Molecular identification by internal transcribed spacer (ITS) regions is required to determine the species identities of the fungal strains.