DNA barcoding can only be used to identify different species when it can distinguish among closely related species, including sister taxa (Newmaster and Ragupathy, 2009). Numerous studies have focused on a large number of plant species with distant genetic relationships. This study is one of the few that evaluated the efficacy of DNA barcoding among congeneric species (Salvia). Although our sampling was limited to a single genus, dense sampling within a genus and within species is necessary to clarify whether DNA barcoding can successfully delineate species rather than only higher taxonomic levels (e.g., to genus or species groups) ( Fazekas et al., 2009 and Pettengill and Neel, 2010). In conclusion, our study shows that ITS1 in the nuclear genome is the best DNA barcoding among the considered loci with sufficient variability and high identification efficiency (81.48%). Although it is not an ideal candidate for all Salvia identification, ITS1 successfully identifies genuine S. miltiorrhiza from common adulterated products which is important and practical in the traditional Chinese medicine market. Furthermore, trnL–F was the most suitable marker in chloroplasts, with an identification efficiency of 77.77%. Further studies should test these sequences on other species, and variable DNA barcodes such as psbK–psbI and atpF–atpH should be used to identify Salvia species.