Wood decay, white-rot and brown-rot fungi have a major economic impact on commercial and manufactured tropical and temperate woods. The aim of this study was to design a molecular method, coupled with PCR and DNA sequencing, to enable early identification of various forms of fungal decay in various types of wood. The resulting tool could be used to certify the healthiness of commercial woods and also to make more efficient use of chemicals and thus reduce their negative environmental impact. Sapwood plates of Distemonanthus benthamianus, Fagus sylvatica, Lophira alata, Pinus sylvestris and Pycnanthus angolensis were incubated in vitro in the presence of Fibroporia vaillantii, Coniophora puteana, Gloeophyllum trabeum, Pycnoporus sanguineus and Trametes versicolor according to the EN 113 standard method. Average weight losses ranging from 2.6 to 25.0% indicated that all wood samples had been actually infected and enabled us to test the reliability of our method. PCR products were obtained in 24 out of 25 combinations and DNA sequences in 21 out of the 24 fungal PCR products. DNA sequences obtained from infected wood were compared with sequences from pure strains, thus confirming the identity of the infecting strains with 100% similarity for an average of 412 bases.