We hybridized the telomere-associated DNA sequence pTel46 isolated from Coprinus cinereus with Helicobasidium mompa genomic DNA. The hybridized fragments were more sensitive to Bal31 nuclease than those that were not hybridized, suggesting that they were located at the ends of chromosomes in H. mompa. The hybridization profile can be used to estimate chromosome number, since the number of chromosomes in a single basidiospore isolate is about half that in putative parent strains. Thus, single basidiospore and field isolates might be homokaryons and heterokaryons respectively. We found telomere-linked restriction fragment length polymorphisms (RFLPs) in strains of H. mompa isolated from field and individual basidiospores. Thus, this marker appears to be an excellent tool with which to reveal the considerable polymorphism of H. mompa and to identify strains. The RFLP was not found among several strains of the same mycelial compatibility group (MCG) isolated from the same field, suggesting that strains belonging to an MCG group are identical.