Complete plastid genomes have recently been proposed as ”super-barcodes” for genetic identification and delineation in plants, for which standard DNA barcodes may fail. However, relatively few studies have fully considered the genetic mechanisms inherent to the taxonomic complexity of specious genera and how this may affect species resolution via complete plastome barcodes. Pedicularis is a highly diversified group of plants whose floral traits have undergone rapid radiation in the Himalaya-Hengduan Mountains, which can complicate identification and classification within the group based on morphological traits alone. In this study, we analyzed 292 plastomes representing 96 species of Pedicularis to compare species discrimination rates with those based on standard DNA barcodes. The results show that the traditional standard barcode (nrITS+matK+rbcL+trnH-psbA) and the large single copy (LSC) region of the plastid genome share the highest discrimination rates (80.21%), followed by the plastid genome, the supermatrixes of protein-coding genes and high variable regions (79.17%), and the matK gene and ycf1 gene alone could discriminate 78.13% of species. Further, we found that the sequence length and percentage of parsimony-informative sites significantly influence species discrimination rates, and genes with higher species discrimination rates are more likely to be conservative in selection. Given the extra costs and time required for generating such “super-barcodes” to try to discern species in taxonomically complex genera, this study questions their use and calls for more efforts to explore nuclear markers that may improve discrimination rates in future studies with relatively low-cost and effort.