The aim of this study was to develop a DNA-barcode assay to authenticate the botanical origin of herbal teas. To reach this aim, we tested the efficiency of a PCR-Capillary Electrophoresis (PCR-CE) approach on commercial herbal tea samples using two non-coding plastid barcodes, the trnL intron and the intergenic spacer between trnL and trnF. Barcode DNA length polymorphisms proved successful in authenticating the species origin of herbal teas. We verified the validity of our approach by sequencing species-specific barcode amplicons from herbal tea samples. Moreover, we displayed the utility of PCR-CE assays coupled with sequencing to identify the origin of undeclared plant material in herbal tea samples. The PCR-CE assays proposed in this work can be applied as routine tests for the verification of botanical origin in herbal teas and can be extended to authenticate all types of herbal foodstuffs.