Abstract: The internal transcribed spacer（ITS）region of nuclear ribosomal DNA（nrDNA）being one of the effective molecular markers was widely used for the phylogenesis of modern molecular biology and species identification. The total DNAs were extracted from the individual cells of three wild Lentinula edodes strains and the nrDNA ITS sequences were amplified，recovered，cloned and sequenced. Then the influence on the phylogenetic tree construction and secondary structure of rRNA were analyzed with these ITS sequences. The results showed that there was relatively high nrDNA ITS diversity in the individual cells of L. edodes，which was suggestive of incomplete concerted evolution. Therefore this result suggested that the ITS sequence was unsuitable for the research on the phylogenies and species identification of L. edodes. However，the further research should be carried on whether there exists such the phenomenon in other fungi.