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An approach was established using RP-HPLC (reversed-phase high-performance liquid chromatography) to identify ten species ofRhodiola, R. coccinea A. Bor, R.junggarica C.Y. Yang et N.R. Cui spn., R. heterodonta A. Bor, R. linearifolia A.Bor, R. pamiro alaiucm A. Bor, R. kaschgarica A. Bor, R. litwinowii A. Bor, R. gelida schrenk, R. rosea L. and R. quadrifide Fisch et Mey collected from the Tianshan Mountains areas of China. Chromatograms of alcohol-soluble proteins, generated from these ten Rhodiola spp. were compared. Each chromatogram of alcohol-soluble proteins came from a single seed of one wild species only. The results showed that when using a Waters Delta Pak. C18, 5 μm particle size reversed phase column (150 mmnx3.9 mm),a linear gradient of 22%-55% solvent B with a flow rate of 1 ml/min and a run time of 67 min, the chromatography gave optimum separation of Rhodiola alcohol-soluble proteins. Chromatogram of each species was different and could be used to identify those species. Cluster analysis of genetic similarity coefficients of 37% to 60% showed a medium degree of genetic diversity among the species in these eco-areas. Cluster analysis showed that the ten species of Rhodiola can be divided into four clusters and yielded the general and unique biochemical markers of these species. RP-HPLC was shown to be a rapid, repeatable and reliable method for Rhodiola species identification and analysis of genetic diversity.