Tugarinovia (Family Asteraceae) is a monotypic genus. It's sole species, Tugarinovia mongolica Iljin, is distributed in the northern part of Inner Mongolia, with one additional variety, Tugarinovia mongolica var ovatifolia, which is distributed in the southern part of Inner Mongolia. The species has a limited geographical range and declining populations. To understand the phylogeographic structure of T. mongolica, we sequenced two chloroplast DNA regions (psbA-trnH and psbK-psbI) from 219 individuals of 16 populations, and investigated the genetic variation and phylogeographic patterns of T. mongolica. The results identified a total of 17 (H1-H17) chloroplast haplotypes. There were no haplotypes shared between the northern (T. mongolica) and southern groups (T. mongolica var. ovatifolia), and they formed two distinct lineages. The regional split was also supported by AMOVA and BEAST analyses. AMOVA showed the main variation that occurred between the two geographic groups. The time of divergence of the two groups can be dated to the early Pleistocene epoch, when climate fluctuations most likely resulted in the allopatric divergence of T. mongolica. The formation of the desert blocked genetic flow and enhanced the divergence of the northern and southern groups. Our results indicate that the genetic differences between T. mongolica and T. mongolica var. ovatifolia are consistent with previously proposed morphological differences. We speculate that the dry, cold climate and the expansion of the desert during the Quaternary resulted in the currently observed distribution of extant populations of T. mongolica. In the northern group, the populations Chuanjinsumu, Wuliji and Yingen displayed the highest genetic diversity and should be given priority protection. The southern group showed a higher genetic drift (FST = 1, GST = 1), and the inbreeding load (HS = 0) required protection for each population. Our results propose that the protection of T. mongolica should be implemented through in situ and ex situ conservation practices to increase the effective population size and genetic diversity.