Analysis of nuclear ribosomal ITS sequence data was used to assess the relationships of Eupatorium godfreyanum, an agamospermous polyploid species of putative hybrid origin. A data set of ITS sequences that included representatives of all but two of the North American species of Eupatorium was compiled from a combination of previously published and newly obtained results. Assessment of the data showed that each species was relatively distinctive, although the results from parsimony analysis suggested that there was little phylogenetic structure within the data beyond a basal split between members of the dog fennel group ("Traganthes") and the remainder of the genus. Cloning was required to obtain readable ITS sequence from E. godfreyanum, and analysis of individual clones produced sequences that matched closely those of either E. rotundifolium or E. sessilifolium. The ITS sequence data thus supported the hypothesis that Eupatorium godfreyanum is of hybrid origin from a combination of E. rotundifolium and E. sessilifolium.