Chloroplast DNA based phylogenetic studies using PCR-amplification and digestion (40 species) combined with Southern blotting (23 species) suggest that Angophora and some representatives of the Eucalyptus subgenera Corymbia and Blakella form a monophyletic group. The subgenera Eudesmia, Monocalyptus, Gaubaea, Idiogenes, Symphyomyrtus and Telocalyptus appear to form a well defined monophyletic group encompassing most of Eucalyptus, but the exact sister taxon to this group remains unresolved. The results suggest that subgenera Corymbia and Blakella are paraphyletic and that Telocalyptus should be submerged within the subgenus Symphyomyrtus.