We investigated the relationship among North American Rhodiola integrifolia Raf., Rhodiola rosea L., and Rhodiola rhodantha (A. Gray) H. Jacobsen by sequencing a fragment of the nuclear-encoded chloroplast-expressed glutamine synthetase (ncpGS) gene from these three species and from selected Asian representatives of the genus. We found that R. integrifolia is a hybrid descendant of R. rosea and R. rhodantha lineages. We also found that the ncpGS gene and the internal transcribed spacer regions of the nuclear ribosomal DNA of Asian Rhodiola algida Fisch. & Mey. are very similar to those of R. rhodantha. In accordance with known chromosome numbers and species morphology, we therefore propose to move R. algida into the subgenus Clementsia of the genus Rhodiola, which so far contains only two species, R. rhodantha and Asian Rhodiola semenovii (Regel & Herder) Boriss.