Breeding lines of Trifolium subterraneum were screened for resistance to root rot caused either by Fusarium avenaceum or Pythium irregulare. One of the tested lines showed good resistance to root rot caused by P. irregulare. High levels of resistance to F. avenaceum were identified in 19 among 50 tested lines. These sources of resistance will be of significant value to breeding programs as few sources of useful resistance in subterranean clover to these pathogens have previously been identified. There were overall significant negative correlations between root rot severity on either tap or lateral roots caused by P. irregulare with shoot dry weight; as there also was between lateral root rot caused by F. avenaceum and shoot dry weight. It is noteworthy that specific resistance to root rot caused by either of the individual pathogens was not linked to survival levels of the seedlings. This indicates that selection of lines for field performance should not only rely on specific resistance to root rot, but also on overall ability of seedlings to survive in the presence of these pathogens.