Thirty-six strains of the fungus Epicoccum nigrum, isolated from different substrata and ecosystems of Europe, America and Africa, were analysed using 14 molecular markers included in 5 different genetic fingerprinting techniques: AP-PCR, tDNA-PCR, microsatellite-primed PCR, ARDRA and AFLP. All of the techniques used were able to differentiate the isolates, showing a high genetic diversity within the species. However, the different techniques detected different levels of similarity among the strains; ARDRA shows the most homogeneous results whilst AP-PCR shows the most heterogeneous. The similarity indices achieved for each strain were compared for the different techniques. The distribution obtained by microsatellite-primed PCR was similar to those shown by AP-PCR techniques. tDNA-PCR and AFLP rendered similar distributions, and ARDRA showed remarkably different results from the other techniques. The results also reveal the lack of an overall correlation between geographical or ecological origin of the isolates and their genotypes.