In the present work we used molecular methods of DNA sequence analyses to investigate two points: first to identify fungal isolates from grapevine and second to determine the phylogenetic positions of these microorganisms. Using partial sequences of the 18S rRNA gene and the 265 rRNA gene yeast isolates have been identified unambigously, with filamentous fungi on the other hand, lack of sequences in the GenBank may lead to unclear results. The phylogenetic tree based on complete 18S rDNA sequences of the division Ascomycota comprises three distinct classes, the Hemiascomycetes, the Protomycetes and the Euascomycetes. Similarly the phylogenetic tree of the division Basidiomycota is tripartite and includes the Urediniomycetes, the Ustilaginomycetes and the Hymenomycetes. The phylogenetic tree clusters all endophytic filamentous fungi from grapevine analyzed so far in different orders of the Euascomycetes. All endophytic yeasts isolates belong either to the Urediniomycetes (Rhodotorula glutinis, Sporobolomyces spec, nov.) or to the Hymenomycetes (Cystofilobasidium macerans, syn. Cryptococcus macerans). The phylogenetic trees of the Ascomycota and Basidiomycota give an overview about presently accepted natural orders of higher fungi In contrast to endophytes of grasses the fungi colonizing grapevine wood show a very remarkable biodiversity of phylogenetically different species.