Fusarium species were isolated from roots, crowns, basal petioles but rarely from the leaves of infected pyrethrum (Tanacetum cinerariifolium) plants showing poor growth and stunting in yield-decline sites of northern Tasmania and the Ballarat region of Victoria, Australia. Multigene phylogenetic analyses using the internal transcribed spacer (ITS), the polymerase II second largest subunit (RPB2) and the partial translation elongation factor 1-α (EF1) sequences, identified F. oxysporum and F. avenaceum as the most frequently isolated species associated with root and crown diseases of pyrethrum, and F. equiseti and F. venenatum at a low incidence. Pathogenicity trials confirmed that F. oxysporum and F. avenaceum significantly affected growth of pyrethrum plants causing Fusarium crown rot; however, F. avenaceum was less pathogenic than F. oxysporum. Fusarium oxysporum and F. avenaceum may be part of a complex of pathogens that are involved in pyrethrum yielddecline.