Several Fusarium species are associated with wheat stems in New Zealand, but there are no detailed reports on the relative abundance and distribution of these species. Hence, a survey was conducted on the South Island of New Zealand to assess the frequency of isolation of Fusarium species associated with randomly collected wheat stem bases and seven grass species. A total of 11 Fusarium species were isolated from wheat stem bases, six of which were also isolated from the other grasses. Putative isolates of the known wheat pathogens F. culmorum and F. pseudograminearum were recovered from wheat and grass stem bases. Fusarium culmorum was isolated from 16% of all wheat stems compared with F. pseudograminearum which was only isolated from 1.5% of the wheat stems. Amplified fragment length polymorphism analysis revealed five distinct clusters among the isolates analysed. These clusters correspond to four pathogenic species, F. pseudograminearum, F. culmorum, F. crookwellense and F. graminearum, based on the sequence of the Tef-1 (translation elongation factor-1α) gene. Isolates from the grass Chionochloa rubra ssp. cuprea which were putatively identified as F. pseudograminearum based on morphological features were found to be isolates of F. graminearum that could not form perithecia homothallically under laboratory conditions. Molecular characterisation confirmed the association of F. pseudograminearum with wheat stem bases, and indicated that there is some genetic divergence between isolates of this important pathogen recovered on the North and the South Islands of New Zealand.