To attract insects for sexual reproduction, some fungi can induce the formation of pseudoflowers on their hosts. Pseudoflowers are rosettes of yellow host leaves upon which the fungus presents gametes in sweet nectar. Eleven species of the fungus complex Uromyces pisi can induce pseudoflowers on the host Euphorbia cyparissias. The taxonomy of these species is based on the choice of the alternate host, a species of Fabaceae, as well as on teliospore morphology on the Fabaceae hosts. Morphological identification of the fungi on E. cyparissias is impossible. To identify the fungal species on infected E. cyparissias, we compared sequences from the ITS region of the rDNA to the DNA from five identified fungal species on Fabaceae. From 43 specimens on E. cyparissias, collected in 1997–99 in Switzerland, 24 specimens could be identified as U. pisi s. str. and 16 specimens as U. striatus. Two specimens were identified as U. laburni and U. loti, respectively, and one specimen could not be identified. We therefore conclude that fungal pseudoflowers are typically induced by U. pisi s. str. on U. striatus in Switzerland, although other species do sometimes occur. The ITS sequences were then used to reconstruct the phylogenetic relationship among species in the U. pisi complex and two closely related microcyclic rust species of the complex Uromyces scutellatus. Phylogenetic analyses indicated that the microcyclic species may be descendants from macrocyclic U. pisi s.l. ancestors. The ITS region sequenced in this study was found to be appropriate for answering phylogenetic, as well as ecological questions, and provided valuable markers for future studies.