The impact of unknowingly including a hybrid or an allopolyploid in which rDNA homogenization (via gene loss, concerted evolution, or some other mechanism) has not occurred to completion in a phylogenetic analysis of internal transcribed spacer (ITS) or external transcribed spacer (ETS) sequences is unclear. To investigate the impact of polymorphic sites on phylogeny reconstruction, we used ITS and ETS sequence data for diploids and allotetraploids in Tragopogon, as well as ITS data for diploid and allopolyploid species of Paeonia and Glycine, and for diploids and their hybrids in Rubus. Only very general predictions can be made regarding the placement of these polymorphic sequences. The polymorphic sequences of hybrids and allopolyploids appear (1) with a diploid parent (but not necessarily the one with which it shares more apomorphies), (2) at or near the base of the clade containing one or both parents, or (3) in a basal position relative to all other ingroup taxa in the data set. The inclusion of a polymorphic sequence may be accompanied by an increase in the number of shortest trees, less resolution in the strict consensus, and a decrease in bootstrap support for some nodes; CI and RI values are little, if at all, affected. In no case did the addition of a sequence from a hybrid or allopolyploid alter the overall topology in a major way. Our results generally parallel those of phylogenetic studies that include F₁ hybrids and their parents and use morphology.