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Genetic variability in the wild genotypes of Salvia miltiorrhiza Bunge.collected from different parts of China, was analyzed using two remarkable single primer amplification reactions(SPAR) markers, viz., Inter-simple Sequence Repeats (ISSR) and Start Codon Targeted (SCoT).A total of seventy-two individuals comprising of nine wild populations were applied to investigate the existing natural genetic diversity.Four hundred and thirty three (458) amplification fragments were scored by thirty-three (33) SPAR primers, which collectively showed a high polymorphism of 86.90% with a mean polymorphie fragments of 13.88.Meanwhile, their level of diversity at inter-and intra-population levels was significant, with the percentage of polymorphic loci (PPB)ranging from 33.03% to 45.27%.Neis gene diversity values (h) varied from 0.124 to 0.167 and Shannons diversity values (I) ranged from 0.183 to 0.247 with a genetic diversity at inter-population level 0.508 and genetic diversity at intra-population level 0.140.The estimate gene flow was 0.483.AMOVA analysis of pairwise distances indicated both high variation at intra-population level (46.26%) and inter-population level (53.74%).Five clusters were detected by cluster analysis using the unweight pair-group method with arithmetic average (UPGMA) and STRUCTURE.This study demonstrated that the efficiency of SPAR methods to assess the genetic diversity of wild Salvia miltiorrhiza populations and can be as strating point for future research on the population and evolutionary genetics of this species.