The efficiency of RAPD analysis in the evaluation of genetic variability in Hypoxylon mediterraneum has been tested on 49 monoascospore isolates of the fungus from different localities. A large genetic variability was detected within single stromata and among monoascospore isolates in a restricted area. The large variability in restricted populations can be explained by the heterothallic mating system and the life cycle of the fungus and its ecological adaptations. RAPD markers can discriminate monoascospore isolates both in the single stromata and among stromata. The application of RAPD markers for epidemiological studies is discussed.