Tanshinone is one of the major medicinal components of the roots of Salvia miltiorrhiza Bunge, and SmCPS1 and SmKSL1 are key enzymes in the tanshinone biosynthesis pathway. To increase our understanding of the coding single nucleotide polymorphisms (cSNPs) involved in tanshinone biosynthesis, seven S. miltiorrhiza landraces were examined. Our results revealed that the tanshinone content was significantly different among the seven landraces. In total, 48 cSNPs in SmCPS1 and 47 cSNPs in SmKSL1 were identified, and of these, 38 and 42 cSNPs, respectively, were associated with tanshinone content. The highest A/G and C/T base substitution rates were in SmCPS1 and SmKSL1, respectively. SmKSL1 expression was significantly, positively correlated with tanshinone IIA and tanshinone I contents, and SmCPS1 expression was significantly associated with tanshinone IIA content. Interestingly, subcellular SmCPS1 and SmKSL1 expression was enriched in the plastids. Therefore, cSNPs of SmCPS1 and SmKSL1 are involved in tanshinone biosynthesis in the plastids, where SmCPS1 and SmKSL1 enzymes catalyze tanshinone production in this species.