Objective:To investigate the relationship between the single nucleotide polymorphism（SNP）of function genes and effective components of Salvia miltiorrhiza and the molecular mechanism of specific quality formation of S. miltiorrhiza. Method:The fingerprints of components in S. miltiorrhiza from eight different habitats and varieties were obtained by high-performance liquid chromatography （HPLC）. The full-length cDNA of three functional genes acetyl-CoA C-acetyltransferase（SmAACT），4-diphosphocytidyl-2-C-methyl-D-erythritol kinase（SmCMK） and isopentenyl diphosphate isomerase（SmIPPI） in tanshinone metabolic pathway were amplified by polymerase chain reaction（PCR），cloned， and sequenced，followed by bioinformatics analysis. Result:The full-length cDNA sequences of three functional genes SmAACT，SmCMK， and SmIPPI in tanshinone metabolic pathway were obtained from 23 strains of S. miltiorrhiza from eight different habitats and varieties. As revealed by the analysis of SNP and amino acid polymorphisms of three functional genes，18，16， and 14 SNP sites were found respectively. HPLC results showed the samples from Beijing，Hubei，Shandong （No. SDB），Shanxi，Henan， and Shandong （No. SDZ） were clustered into one branch，and those from Hebei and Inner Mongolia were clustered into another branch， which suggested that the variation trend of S. miltiorrhiza components had little correlation with geographical distance，but the variety was a critical factor for the quality. Conclusion:There was an obvious genetic differentiation trend in S. miltiorrhiza from different habitats，and different origin-specific genotypes were formed. The molecular mechanism of the formation of the specific quality of S. miltiorrhiza from different habitats was discussed，which laid a foundation for the stability and effectiveness of clinical medication，and guided the breeding of excellent varieties of S. miltiorrhiza.