The internal transcribed spacer (ITS) of the nuclear ribosomal DNA (rDNA) of the main fungal species causing wood rot damages in European buildings was amplified by the polymerase chain reaction (PCR). After sequencing the ITS, fungus-specific oligonucleotide primers were designed for taxon-specific priming PCR. These DNA marker molecules were suitable for the differential diagnosis of the Dry rot fungus, Serpula lacrymans , the Wild merulius, S. himantioides , the Oak polypore, Donkioporia expansa , the Brown cellar fungus, Coniophora puteana , the Broad-spored white polypore, Antrodia vaillantii , the Sap polypore, Tyromyces placenta , and the Yellow-red gill polypore, Gloeophyllum sepiarium . Each specific marker identified isolates of its respective target species. Cross reaction with ‘foreign’ fungi was the exception. Species detection from rot samples in buildings was possible, since DNA from contaminating organisms does not response to the marker molecules. The diagnosis was rapid, since preceding fungal pure cultures, special DNA extraction/purification and restriction by endonucleases are not required.