Rhodiola (Crassulaceae) comprises about 70 species and shows a high level of morphological diversity. The genus is mainly distributed in alpine areas and cold regions of the Northern Hemisphere with the Qinghai-Tibetan Plateau as its center of diversity. The phylogenetic relationships within Rhodiola remain poorly understood largely because of difficulties in collecting samples and specimens. In the present study, 51 species/varieties from Rhodiola representing all morphological sections were analyzed using sequences of the nuclear ribosomal internal transcribed spacers region and the plastid psbA-trnH and trnL-F markers. Our results suggest that Rhodiola and Pseudosedum form a well-supported clade, but the relationship between these two genera is not resolved. None of the four currently recognized subgenera is monophyletic; yet three of seven sections, R. sects. Trifida, Prainia, and Pseudorhodiola are each supported to be monophyletic. Rhodiola rosea is a popular medicinal plant that has an adaptogenic effect. The three accessions of R. rosea from eastern Asia, eastern North America, and Europe form a well-supported clade. Rhodiola species independently reached North America from Asia twice, once in the R. rosea lineage, and the other in the R. integrifolia-R. rhodantha lineage. Two taxonomically important characters, dioecy and marcescent flowering stems, are inferred to have evolved multiple times within Rhodiola.