Abstract:In this test, SSR loci were searched for the mitochondrial and chloroplast genome sequences of Salvia miltiorrhiza by bioinformatics methods, and the SSR primers were designed by primer3.0 online software. 10 pairs of cpSSR primers and 13 pairs of mtSSR primers with high polymorphism were selected by PCR amplification. They were used to analyze the genetic diversity of 61 S. miltiorrhiza cultivars and the transferability of Salvia L. species.(1) Total 32 cpSSR and 24 mtSSR were identified from 2 genome sequences. There were 31 mononucleotide repeat sequences with 96.9% frequency, showing the dominant types in the cpSSR. Both A/T types were abundant among mononucleotide repeat sequences.(2) 46 alleles were detected in 23 pairs of SSR primers, the average number of alleles per SSR locus was 2, and the number of effective alleles was 1.566. The expected heterozygosities was 0.346, which was higher than the average level of dicotyledons (He=0.190); the polymorphism information content was 0.278, which was between 0.250 and 0.500; Shannons information index was 0.519. The results showed that S. miltiorrhiza had a moderate level of genetic diversity.(3) The cluster analysis on 61 S.miltiorrhiza showed that the genetic similarity coefficient was ranging from 0.54 to 0.96. It can be divided into 6 subgroups when the genetic similarity coefficient was 0.64: the S.miltiorrhiza in Sichuan, Shandong and Anhui provinces clustered in Ⅰ and Ⅱ subgroups, suggesting their close relationship. S.miltiorrhiza in Zhongjiang of Sichuan Province were distributed in all the subgroups, suggesting their rich polymorphism.(4) The results of transferability test showed that 11 pairs of mtSSR primers were successfully amplified in nine species belong to Salvia L., the transferability ratio was 64.63%, suggesting mtSSR markers showed a higher transferability. 9 pairs of cpSSR primers were successfully amplified in all samples of Salvia.L. species, and the transferability ratio was 44.66%, suggesting cpSSR markers showed a lower transferability. In addition, the primers cp5p, cp8p and cp10p had good generality among the genera of Lamioideae. These results indicated that 23 primers are suitable for SSR analysis of Salvia L. It would be useful for species relationship and study of genetic variation of Salvia L..