Cymbaria L. is a small genus nearly endemic to the Mongolian Plateau with only two hemiparasitic species. Cymbaria daurica L. is an important herb “Xinba” in traditional Mongolian medicine. However, C. daurica is often confused with its sister species Cymbaria mongolica Maxim. because they only differ in anther morphology. In addition, phylogenetic placement and reductive evolution of this genus within the Orobanchaceae remain poorly resolved. Here, we firstly sequenced two Cymbaria chloroplast genomes and then conducted a comparative analysis among those of 54 Orobanchaceae species. We found that the chloroplast genomes of Cymbaria species were characterized by pseudogenization/loss events of eight ndh genes and a unique rbcL-matK inversion. Unlike the high-variability observed in holoparasites, Cymbaria and other hemiparasites exhibited high similarity to autotrophs in genome size, GC content, and intact genes. Notely, four pairs of specific DNA barcodes (CymN1, CymN2, CymY, and CymR) were developed to distinguish the herb C. daurica from its adulterant C. mongolica. Phylogenetic analyses revealed that genus Cymbaria and the Schwalbea-Siphonostegia clade were grouped into the tribe Cymbarieae. This tribe formed an independent sister clade to the remaining parasitic lineages. Furthermore, the diversification of monophyletic Cymbaria occurred during the late Miocene (6.72 Mya) in the Mongol-Chinese steppe region. These findings provide valuable information for regarding taxonomy, phylogeny and evolution of Cymbaria and can be used to validate the authenticity of the herb “Xinba”.