Phylogenetic analyses can be used in order to obtain the evolutionary relationship and evolutionary distances among the species of fungi. Molecular phylogenetic analyses of ITS regions (ITS1; 5.8S rDNA; ITS2) of ribosomal DNA of filamentous fungi from four deteriorated old Chinese manuscripts in Central Library Universitas Indonesia was conducted to obtain information of the phylogenetic relationships among the species, closely related species, species diversity, and taxonomic position. Phylogenetic tree construction from the ITS regions was performed using methods of Neighbor-Joining, Maximum Likelihood, and Minimum Evolution with Kimura's two-parameter model, and bootstrap 1,000 replicates. Eleven fungal strains belonged to three classes (Dothideomycetes, Eurotiomycetes and Sordariomycetes), five orders (Capnodiales, Eurotiales, Hypocreales, Pleosporales, and Xylariales), six families (Aspergillaceae, Cladosporiaceae, Microdochiaceae, Ophiocordycipitaceae, Pleosporaceae, and Trichocomaceae), six genera (Aspergillus, Cladosporium, Curvularia, Penicillium, Purpureocillium, and Sarocladium), and three closely related species (Aspergillus pseudodeflectus, Penicillium coffeae, and Purpureocillium lilacinum syn. Paecilomyces lilacinus). The ITS sequences of other strains were not identical to any type strains. Further studies using multiple locus analyses are required to confirm the species identities of these strains.