Comparative plastome analyses and phylogenetic reconstruction were used to investigate the phylogenetic position of Peucedanum muliense. Comparative analyses showed that the plastome features of Peucedanum muliense were highly similar to those of nine species from the genus Ligusticopsis but differed from Peucedanum morisonii in terms of the location of genes at the IRa/LSC boundary, codon usage bias in terminator T/A, and sequence diversity exhibited by numerous gene regions. Phylogenetic reconstructions indicated that Peucedanum muliense does not cluster with Peucedanum s.s., but is nested with species of the genus Ligusticopsis, and that the four accessions of Peucedanum muliense formed a separate branch in the nrITS phylogenetic tree. The external morphology, pinnate bracts and pinnate bracteoles longer than umbellules of Peucedanum muliense are also consistent with those of the genus Ligusticopsis. We conclude that Peucedanum muliense does not belong to Peucedanum s.s., but should be transferred into the genus Ligusticopsis as an independent species. Therefore, the new combination, Ligusticopsis muliensis, is proposed here.