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Pueraria genus [Pueraria lobata (Willd.) Ohwi and Pueraria thomsonii Benth] are widely distributed and used as health food in China and other Asia countries. However, the root and flower of two Pueraria species are commonly used as substitutes for each other and may adversely affect consumer health, as it could cause efficacy instability or not have the intended effect. In the present paper, ultra-performance liquid chromatography-electrospray ionization mass spectrometry (UPLC-ESI-MS) with relative quantitative heatmap analysis and molecular docking experiment was established for simultaneous determination of eleven chemical markers (i.e., 3′-hydroxy puerarin, puerarin, 3′-methoxy puerarin, puerarin xyloside, daidzin, genistin, tectoridin, ononin, daidzein, genistein, and tectorigenin). Based on obtained data, a method based on quantitative analysis of multi-components by single marker (QAMS) for quality evaluation of both species in detail has been developed. Then, a total of forty batches of roots and flowers covering two Pueraria species were processed using QAMS and multivariate statistical analysis. In conclusion, this study not only established a method of simultaneous determination of multiple bioactive constituents in the root and flower from different batches of Pueraria species, but also provided detailed profiles of their chemical differences of them.

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