AbstractHere we present the first nuclear phylogeny for Cystopteridaceae (Polypodiales), using the single‐copy locusgapCp“short”. This phylogeny corroborates broad results from plastid data in demonstrating strong support for the monophyly of the family's three genera—Cystopteris, Acystopteris, andGymnocarpium—and of the major groups withinCystopteris(C. montana, the sudetica and bulbifera clades, and theC. fragiliscomplex). In addition, it confirms the rampant hybridization (allopolyploidy) that has long been suspected within bothCystopterisandGymnocarpium. In some cases, these data provide the first DNA‐sequence‐based evidence for previous hypotheses of polyploid species origins (such as the cosmopolitanG. dryopterisbeing an allotetraploid derivative of the diploidsG. appalachianumandG. disjunctum). Most of the allopolyploids, however, have no formal taxonomic names. This pattern is particularly strong within theC. fragiliscomplex, where our results imply that the eight included accessions of “C. fragilis” represent at least six distinct allopolyploid taxa.