In this paper, the internal transcribed spacer (ITS) regions of nuclear ribosomal DNA(nrDNA) were sequenced from six species of Rhodiola in Yunnan. The sequences of the ITS regions ranged from 604 to 617 base pairs (bp). Using Sedum bulbiferum as the outgroup, phylogenetic trees of 22 Rhodiola species were constructed with the maximum parsimony (MP) and the neighbor-joining (NJ) methods. Two clades were then classified in both MP and NJ trees with relatively high bootsrap values.