To study the genetic relationship of Astragalus membranaceus var. mongholicus in different producing area and provide theoretical basis for the evaluation of Astragalus germplasm resources.Through quence-related amplified polymorphism (SRAP) analysis, the systematic diagram of genetic relationship was constructed by UPGMA method.A total of 141 SRAP markers were scored. By the use of UPGMA cluster analysis with genetic distance, Astragalus could be divided into two provenance plots of Gansu and Shanxi.The genetic differentiation among populations of A. membranaceus var. mongholicus is remarkable. SRAP marker could be efficiently used for the study of the genetic relationship of Astragalus.