Ferns are one of the three main clades of vascular plants. They have few easily studied morphological characters, reflected in a historically unstable classification. The fern genus Woodsia is known to have a complex evolutionary history including numerous polyploid taxa and hybrids. It is a cosmopolitan group of small rock loving ferns mainly found in montane areas. This thesis aims at analyzing the patterns of diploid and polyploid evolution in Woodsia and to resolve and classify the relationships of Woodsiaceae and the other families in the large fern clade Eupolypods II. The Eupolypods II family relationships were inferred with DNA sequences from 81 specimens representing all major lineages. This resulted in the first well supported phylogeny of this clade and revealed Woodsiaceae to be non-monophyletic. The genera previously placed in this family were reclassified into five new or resurrected families. Swedish fern genera that have changed family classification are Woodsia (hällebräknar), now in the monogeneric family Woodsiaceae, Athyrium (majbräknar), now  in Athyriaceeae and Cystopteris (stenbräknar) and Gymnocarpium (ekbräknar) now in Cystopteridaceae. To analyze the evolution of Woodsia, phylogenies were produced from five plastid and two nuclear regions sequenced from 188 specimens. The results show that most taxa in Woodsia are polyploid. Polyploidization is the most common mode of speciation in the genus with an estimated polyploid speciation rate of 54%. The polyploids are mostly young and many of the polyploid taxa seem to have formed multiple times. The results also address several taxonomic and biogeographic questions. In the process of the work we made methodological advancements and developed 20 new low copy nuclear marker regions as well as a software pipeline for finding primers in transcriptome datasets. The alignment editor software AliView was developed for handling the increasing size datasets in a user friendly way. In conclusion this thesis provides new insights into the complexities of the evolution of a fern genus in which much of the diversity is accommodated in young species formed through polyploidization. It provides a framework of phylogenetic relationships at different levels that both answers long standing questions and generates new ones.