We investigated the phylogenetic affinities of the following six taxonomically anomalous species of Eucalyptus: E. cladocalyx, E. cosmophylla, E. gomphocephala, E. longifolia, E. paludicola and E. pumila. ITS sequence data were obtained from these species and combined with an existing large ITS data set for subgenus Symphyomyrtus. Phylogenetic analysis using maximum parsimony and Bayesian approaches showed that E. longifolia belongs in section Maidenaria and E. gomphocephala belongs in section Bisectae I. The phylogenetic affinities of the other four species were not fully resolved by ITS sequence data. E. cladocalyx has affinities with sections Adnataria, Dumaria and Bisectae I; E. cosmophylla and E. paludicola have affinities with sections Exsertaria, Latoangulatae and Maidenaria; and E. pumila appears to be a morphologically divergent member of section Latoangulatae or Exsertae. The implications of the results for conservation of native eucalypt gene pools are discussed.