Rusts (Basidiomycetes: Uredinales) are a large, diverse group of obligate biotrophic fungi that include many important plant pathogens. Phylogenetic relationships within the group are poorly understood, with between two and 14 families being recognised on morphological and host taxonomic grounds. We report the first analysis of broad-scale relationships within the Uredinales using DNA sequence data from the small subunit gene of the rRNA operon. A major split is obvious between genera that have aecial stages on gymnosperm hosts and those with this stage on angiosperms. This finding is in accord with the early taxonomic two-family treatments of the Uredinales. Within the major clades, there is evidence of in congruency with morphologically defined families. Racospermyces, Maravalia, Hemileia and Caeoma are basal to the major phylogenetic sub-division and probably represent the most ancient rust lineages. Using these sequence data, we estimate that the rusts diverged from their closest relatives around 150 million years ago.