It is important to identify wood rotting fungi and fungal flora in building materials to properly maintain wooden houses. The objective of this study is to identify filamentous fungi in wooden foundations by performing a DNA sequencing analysis of internal transcribed spacer regions of ribosomal DNA obtained from methods for denaturing gradient gel electrophoresis and clone libraries. The results of the study illustrate the majority of detected fungi share the highest homology with Uncultured Basidiomycota. Furthermore, a phylogenetic tree analysis revealed the taxonomic positions of these fungi.