Nuclear ribosomal DNA (nrDNA) has been used for more than a decade in species level phylogenetic analyses. While nrDNA can often be a powerful phylogenetic marker, intraindividual polymorphisms of the internal and external transcribed spacers (ITS, ETS) can lead to problems in their use for phylogeny reconstruction. Incomplete concerted evolution coupled with hybridization and incomplete lineage sorting can further exacerbate these problems. Previous phylogenetic analyses using nrDNA of Carex subgenus Vignea suggest that the current sectional classifications may be highly artificial. We endeavored to identify what influence incomplete concerted evolution, lineage sorting, and hybridization have played in the complex patterns of relationships previously inferred from ITS and ETS sequences for subgenus Vignea. Through comprehensive cloning we identified high levels of intraindividual polymorphisms and in many cases this led to the polyphyly of individuals. Furthermore, individuals identified with novel mutations in the 5.8S ribosomal subunit did not show a significant deviation in G-C percentage and free energy. Based on these results we suggest that nrDNA contains multiple paralogs in many species and clades within Carex subgenus Vignea which greatly complicates its use for phylogenetic inference of relationships and future studies in Carex need to take this into account.