Pleistocene climate fluctuations had profound influence on the biogeographic history of many biota. As large areas in higher latitudes and high mountain ranges were covered by glaciers, biota were forced either to peripheral refugia (and possibly beyond to lowland refugia) or to interior refugia (nunataks), but nunatak survival remains controversial as it solely relies on correlative genetic evidence. Here, we test the nunatak hypothesis using two high alpine plant species of contrasting pollination modes (insect-pollinated Pedicularis aspleniifolia and wind-pollinated Carex fuliginosa) in the European Alps, a geographic model system to study Pleistocene biogeography. Employing the iDDC (integrative distributional, demographic and coalescent) approach, which couples species distribution modelling, spatial and temporal demographic simulation and Approximate Bayesian Computation, we explicitly test three hypotheses of glacial survival: (1) peripheral survival only, (2) nunatak survival only, and (3) nunatak plus peripheral survival. In P. aspleniifolia the nunatak plus peripheral survival hypothesis was supported by Bayes Factors (BF > 100), whereas in C. fuliginosa the peripheral survival only hypothesis, though best supported, could not be unambiguously distinguished from the nunatak plus peripheral survival hypothesis (BF = 5.58). These results are consistent with current habitat preferences (P. aspleniifolia extends to higher elevations) and the potential for genetic swamping, i.e., replacement of local genotypes via hybridization with immigrating genotypes (expected to be higher in the wind-pollinated C. fuliginosa). Although the persistence of plants on nunataks during glacial periods has been debated and studied over decades, this is one of the first studies to explicitly test the hypothesis instead of solely using correlative evidence.