DNA barcodes are short parts of DNA used to identify an unknown specimen of the species. DNA barcodes have been used in associating the stages of life, determining cryptic species, preventing illegal trade, etc. Herein, we used two DNA barcodes, trnH-psbA intergenic spacer and matK region to discriminate endemic Ida Mountain Sideritis trojana B. plant. We assessed the genetic relatives of S. trojana with the other Lamiaceae, and compared the classical taxonomic classifications of the species with the classifications obtained through DNA barcode trees. matK was found to be more suitable for DNA barcoding study because of the easiness of the alignment and constructing the tree. matK was generally enough to discriminate species. It can be used as a core barcode but in the identification-based DNA barcode investigations, combination of matK with a more variable region can be suggested.