AbstractKingdonia uniflora, an alpine herb, has an extremely narrow distribution and represents a model for studying evolutionary mechanisms of species that have adapted to undisturbed environments for evolutionary long periods of time. We assembled a 1,004.7-Mb draft genome (encoding 43,301 genes) and investigated the evolutionary history ofK. uniflora, along with mechanisms related to its endangered status. Phylogenomic analyses based on 497 single copy genes confirmed the sister relationship betweenK. unifloraandCircaeaster agrestis, which were estimated to have diverged around 52 Mya. Proliferation of LTR retrotransposons inK. uniflorais estimated to occur around 2.7 Mya, coinciding with one recent uplift of the Hengduan Mountains between the late Miocene and late Pliocene. Across 12 species of monocots, early-diverging eudicots and core eudicots,K. uniflorashowed significant overrepresentation in gene families associated with DNA repair and underrepresentation in gene families associated with stress response. Most of the plastidndhgenes were found to be lost not only in the plastome but also in the nuclear genome ofK. uniflora. During the evolutionary process, the overrepresentation of gene families involved in DNA repair could help asexualK. uniflorareduce the accumulation of deleterious mutations, while at the same time, reducing genetic diversity which is important in responding to environment fluctuations. The underrepresentation of gene families related to stress response and functional loss ofndhgenes could be due to lack or loss of ability to respond to environmental changes caused by long-term adaptation to a relatively stable ecological environment.