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Molecular species discrimination is significant where traditional taxonomic approaches fail. To overcome the limitations of conventionalbarcoding loci, plastid genome (plastome) and nuclear ribosomal DNA (nrDNA) sequencesrecovered from genome skimming,proposed as "super-barcodes," have been suggested as candidates for delimitating recently diverged species or complex plant groups. DNA super-barcodes must be assessed for their effectiveness in additional diverse plant species. In this research significant but taxonomically complex genus Codonpsis, complicated by the simple morphology and trends toward environmental plasticity. We analyzed multiple data sets, including standard DNA barcodes and super-barcodes, across 81 individuals from 36out of 42 species of Codonopsis from Asia.