Polymorphisms of a ribosomal DNA region (ITS) have been analysed using a specific pair of primers, in order to type fruitbodies and ectomycorrhizae of different truffle species. The identification of ectomycorrhizae was obtained by digestion of the PCR products using restriction enzymes. The resultsshow that the strategy used is both suitable and sensitive to characterize the symbiotic fungi from few mycorrhized root tips.