DNA sequences from five chloroplast DNA regions (the rpl16 and rps16 introns and the psbA–trnH, ycf4–cemA, and trnT–L spacers), and the nuclear ribosomal internal and external transcribed spacer (ITS and ETS) regions, were analyzed using maximum parsimony and Bayesian methods to explore the putatively complicated history of the mainly North American genus Arnica. The chloroplast regions were found to contain minimal variation in Arnica. Of 3710 nucleotides, only 119 were variable and 45 informative. However, combined with the ribosomal DNA data, the analysis yielded a number of well-supported clades. Strong support for the monophyly of Arnica was found in both the separate and combined analyses but none of the five currently recognized subgenera was resolved as monophyletic in any of the analyses. Arnica (Whitneya) dealbata and A. mallotopus (Mallotopus japonicus), two species that were previously placed outside Arnica, were confidently confirmed as members of the genus. The analyses revealed that A. nevadensis (subg. Austromontana) is most closely related to A. dealbata and that A. mallotopus forms a strongly supported clade with A. unalaschcensis (subg. Andropurpurea). Earlier biogeographical hypotheses that suggested an arctic origin and southward spread of the genus are not supported by our analyses. Hybridization, homoplasy, and rapid evolution are possible explanations for conflicts between the chloroplast and nuclear ribosomal data sets and for low support of the deeper nodes.