We amplified by PCR and sequenced 46 partial Ty1- copia reverse transcriptase (RT) sequences from the ectomycorrhizal basidiomycetes Pisolithus and Laccaria bicolor and the host tree Eucalyptus globulus. Phylogenetic analyses indicated that these sequences represent a new class of Ty1- copia RT, characteristic of basidiomycetes but related to plant Ty1- copia retrotransposons. To generate fingerprints of L. bicolor strains, outward facing PCR primers annealing to RTs were designed. This method, which is a modification of the inter-retrotransposon amplified polymorphism (IRAP) analysis, enables the detection of polymorphisms or changes within the insertion sites of Ty1- copia elements in the genome. Using this method, we investigated whether the transposition of Ty1- copia elements was related to the somaclonal variation observed in L. bicolor S238, an inoculant strain used in French Douglas-fir plantations. Data indicated that no differences in the IRAP fingerprints were detected in phenotypic variants of L. bicolor S238. We reported here for the first time the presence of Ty1- copia retrotransposon sequences in basidiomycetes, which resulted in suitable targets for developing new molecular markers.