Climate change is projected to influence the genetic resources of plant species. Recent research has examined genetic diversity patterns under current climate conditions, with little attention to the future genetic consequences for species. In this study, we combined ecological niche modeling and population genetic approaches to project future changes in genetic diversity using plastid and nuclear DNA and reconstructed distribution patterns of three circumboreal plants (Chamaedaphne calyculata, Linnaea borealis ssp. borealis, and Pedicularis sceptrum-carolinum ssp. sceptrum-carolinum) in the last glacial maximum. We found that circumboreal plants could potentially lose their geographic ranges in the future (2070; 35–52% in RCP 4.5 (representative concentration pathways), 37–53% in RCP 6.0, and 56–69% in RCP 8.5), only slightly compensated by a predicted range gain of 18–33% (across the three RCPs). It is expected that future genetic diversity level could remain similar or lower than the present level. On the other hand, the homogeneity of the genetic background—a lack of admixture and domination of one gene pool in most populations of C. calyculata and L. borealis ssp. borealis—was predicted to become more pronounced in the future. Combining the paleoecological niche modeling and genetic data revealed, more precisely, the climate refugia for circumboreal plants in the Alps, central Asia, Beringia, and southern North America and the macrorefugia more restricted to the northern part of Eurasia and North America, reaching the arctic zone.