Twenty-seven Fusarium oxysporum isolates were studied by RAPD-PCR and isozyme analyses. Thirteen isolates were from barley and the rest from different hosts, most of which were dicotyledonous plants. All isolates could be distinguished from each other by RAPD-PCR analysis, and clustered into seven groups in NJ and parsimony consensus trees. Isozyme analysis detected polymorphism in five of the six enzymes and the isolates could be divided into 26 different electrophoretic groups. Five groups were supported by high branch support and bootstrap values in the approximate support tree of combined RAPD-PCR and isozyme data. These five groups were found also in NJ and parsimony consensus trees. The matrices from RAPD-PCR and isozyme data proved to be incongruent, but they did not totally disprove each other. Some correlation was found between geographical origin and phylogenetic relationships of isolates collected from barley. Representatives of the main clades of phylogenetic trees, were further studied by rDNA RFLP and rDNA sequence analyses, together with isolates of other Fusarium species. Isolates of F. oxysporum and F. avenaceum formed distinct groups in the phylogenetic analyses, except for two isolates of F. oxysporum which were grouped with isolates of F. redolens.