Morphological similarity within species makes the identification and authentication of Salvia species challenging especially in dietary supplements that contain processed root or leaf powder of different sage species. In the present study, the species discriminatory power of two potential DNA barcode regions from the nuclear genome was evaluated in seven medicinally important Salvia species from the family Lamiaceae. The nuclear internal transcribed spacer (ITS2) and the exon 9-14 region of low copy nuclear gene WAXY coding for granule-bound starch synthase (GBSS1) were tested for their species discrimination ability using distance, phylogenetic and BLAST based methods. A novel two-step PCR method with two different annealing temperatures was developed to achieve maximum amplification from genomic DNA. The GBSS1 region showed higher amplification and sequencing success rates along with higher interspecific distances and a perfect barcode gap for the tested species as compared to ITS2. Hence, these novel mini-barcodes generated from low copy nuclear gene regions - GBSS1 that were proven to be effective barcodes for the identification of seven Salvia species, have potential for identification and authentication of other Salvia species too.