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Subgenus <i>Perovskia</i> of the extended genus of <i>Salvia</i> comprises several Central Asian medicinal and aromatic species, of which <i>S. yangii</i> and <i>S. abrotanoides</i> are the most widespread. These plants are cultivated in Europe as robust ornamentals, and several cultivars are available. However, their medicinal potential remains underutilized because of limited information about their phytochemical and genetic diversity. Thus, we combined an ultra-high performance liquid chromatography quadrupole time of flight mass spectrometry (UHPLC-QTOF-MS) based metabolomics with DNA barcoding approach based on <i>trnH</i>-<i>psbA</i> and ITS2 barcodes to clarify the relationships between these two taxa. Metabolomic analysis demonstrated that aerial parts are more similar than roots and none of the major compounds stand out as distinct. Sugiol in <i>S. yangii</i> leaves and carnosic acid quinone in <i>S. abrotanoides</i> were mostly responsible for their chemical differentiation, whereas in roots the distinction was supported by the presence of five norditerpenoids in <i>S. yangii</i> and two flavonoids and one norditerpenoid in <i>S. abrotanoides</i>. To verify the metabolomics-based differentiation, we performed DNA authentication that revealed <i>S. yangii</i> and <i>S. abrotanoides</i> to be very closely related but separate species. We demonstrated that DNA barcoding coupled with parallel LC-MS profiling constitutes a powerful tool in identification of taxonomically close <i>Salvia</i> species.