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To test the taxonomy of medical Astragalus penduliflorus complex and specific status of A. petrovii, eleven accessions (covering four species) in China were sampled herein for an AFLP study. A total of 346 informative polymorphic bands from eight primers pairs were obtained, dendrogram was generated using UPGMA analysis. The results indicated A. membranaceus is more morphologically and generically diverse than A. mongholicus on the populational level. Both of them and the former species A. minhensis were degraded as three varieties of A. penduliflorus. In the light of morphological and cladistic evidence, a new combination, A. penduliflorus ssp. mongholicus var. petrovii was proposed based on former species A. petrovii.