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The root and rhizome of Salvia miltiorrhiza (Danshen in short) is a well-known herbal medicine used to treat cardiovascular diseases in the world. In China, the roots and rhizomes of several other Salvia species (Non-Danshen in short) are also used as this medicine in traditional folk medicine by local herbalists. Differences have been reported in these medicines originating from different sources, and their quality variation needs to be clearly investigated for effective clinical application. This study presented a comprehensive quality evaluation and monitoring for Danshen from 27 sampling sites and Non-Danshen from other 5 Salvia species based on a high-performance liquid chromatography-diode array detector (HPLC-DAD) and near-infrared (NIR), with the combination of chemometric models. The results showed that cryptotanshinone, tanshinone IIA, tanshinone I, salvianolic acid B, salvianic acid A sodium, dihydrotanshinone I, and rosmarinic acid in these medicines from different sources exhibited great variations. Referring to the standards in Chinese Pharmacopoeia (CP), European Pharmacopeia (EP), and United States Pharmacopeia (USP), Non-Danshen from S. brachyloma, S. castanea, S. trijuga, S. bowleyana, and S. przewalskii were assessed as unqualified, and Danshen in the Shandong Province had the best quality due to the high qualified rate. Based on random forest (RF) and partial least-squares discriminant analysis (PLS-DA), NIR technique could successfully monitor the quality of these medicines by discriminating the species and regions with the accuracies of 100.00 and 99.60%, respectively. Additionally, modified partial least-squares regression (MPLSR) models were successfully constructed to investigate the feasibility of NIR fingerprints for the prediction of the quality indicators in these medicines. The optimized models obtained the best results for the total of tanshinone IIA, tanshinone I, and cryptotanshinone (TTC), tanshinone IIA, and salvianolic acid B, with the relative prediction deviation (RPD) of 4.08, 3.92, and 2.46, respectively. In summary, this study demonstrated that HPLC-DAD and NIR techniques can complement each other and could be simultaneously applied for evaluating and monitoring the quality of Danshen medicines. [ABSTRACT FROM AUTHOR]