Nuclear rDNA from 120 isolates of 34 Fusarium spp. and Microdochium nivale was compared by restriction fragment length polymorphism (RFLP) analysis after polymerase chain reaction amplification. The RFLPs allowed differentiation between species or groups of species. The presence of absence of each of 75 DNA bands was also used to compile a similarity matrix for cluster analysis to show estimated phylogenetic relationships. There was mostly little diversity between isolates of the some species. However; there were at least two distinct genetic types among isolates that conformed morphologically to each of the species F. avenaceum, F. sambucinum, F. flocciferum, and F. proliferatum. Most relationships were consistent with current understanding of Fusarium taxonomy. The division into taxonomic sections based on morphological characteristics was generally not supported.