The focus for the first part of the thesis is on the systematics of species belonging to Silene subgenus Silene. Phylogenetic relationships are inferred from DNA sequences from both the plastid (the rps16 intron) and the nuclear (ITS, intron of the RPB2 gene) genomes. Silene section Rigidulae is shown to be non-monophyletic in its previous circumscription, but instead consisting of six separate clades, each correlated to the geographical distribution of the included species. The taxonomic consequences for each clade are discussed. One of the clades is recognized as a new section and described as Silene sect. Arenosae sect. nov. The morphological descriptions of the species are formalized using a novel implementation of the Prometheus Description Model. Two proposals are included in the thesis, one to reject the name Silene polyphylla L., which is a senior synonym to S. portensis L. Silene linearis Decne. is proposed for conservation against the rarely used S. linearis Sweet. Silene antirrhina, a weedy American annual, is strongly supported as sister to the Hawaiian endemic species of Silene, suggesting an American origin for these. Two of the endemics have evolved woodiness after introduction to Hawaii. In the second part of the thesis we use four nuclear DNA regions, (introns from RPA2, RPB2, RPD2a, RPD2b), and the chloroplast psbE-petG spacer. A framework is developed to evaluate different phylogenetic explanations for conflicting gene trees, where divergence times are used to discriminate among inter- and intralineage processes. The incongruences observed regarding the relationships among the three major lineages of Heliosperma are best explained by homoploid hybridization. The pattern regarding the origin of Heliosperma itself is more complicated and is likely to include several reticulate events. Two lineages have probably been involved in the origin of Heliosperma, one leading to Viscaria and Atocion and the other to Eudianthe and/or Petrocoptis.