A climate relict is of particular importance in evolutionary biology because of its long-term survival in the face of climatic oscillations. However, because their current distributions are usually restricted and fragmented, many climatic relicts have extinction risks. Daphnimorpha (Thymelaeaceae) is a Japanese endemic genus that comprises two species (D. capitellata and D. kudoi) showing a disjunct distribution in the southern part of Japan. These two species are endemic to a single mountain range. In this study, we conducted population genetic analyses using genome-wide single nucleotide polymorphism obtained from multiplexed inter-simple sequence repeat genotyping by sequencing to reveal the phylogeographic history and obtain conservation implications for the two species. The results showed these two species may have been isolated since the Tertiary period, indicating that they are climate relicts. In addition, D. kudoi showed clear genetic differentiation between two mountains (Mt. Nagata and Mt. Kuromi), with a decline in effective population sizes during the last glacial period. In contrast, D. capitellata showed no clear intraspecific genetic structure and its effective population size was relatively stable. These differences could be a result of differences in habitat preferences between the species. For conservation, we should manage the two species based on the three evolutionary significant units (ETUs; D. capitellata, D. kudoi population on Mt. Nagata, and D. kudoi population on Mt. Kuromi). Considering the limited gene flows among subpopulations and their small population sizes, all ETUs require conservative attention to maintain or increase their effective population sizes.