By using high-performance liquid chromatography-photodiode array detection, a simple andaccurate chromatographic fingerprint method was developed for the identification of RadixCodonopsis (roots of Codonopsis) from different sources. Eighteen herbs of Codonopsis at differenthabitats in China, including roots from Codonopsis pilosula, Codonopsis pilosula var. modesta andCodonopsis tangshen were analyzed by the fingerprint. The amount of lobetyolin was calibrated,which was found to be more consistent in roots of Codonopsis pilosula as compared to that ofCodonopsis pilosula var. modesta and Codonopsis tangshen. Having the fingerprint results, hierarchicalclustering analyses were performed to classify the eighteen herbs into three groups: Codonopsispilosula, Codonopsis pilosula var. modesta and Codonopsis tangshen. This clustering analysis agreesvery well with the pharmacognostic identification result, and which could be used as a tool in thequality control of Radix Codonopsis.