Reconstruction of the glacial and postglacial history of a species, including life-history traits, provides valuable insights into the relationships between ecological and genetic factors shaping phylogeographic patterns. Clonality appears as a trait of high importance for survival in northern refugia. In the present study, the phylogeographic structure of 24 Alnus incana (grey alder) populations and clonal structure in seven populations were analyzed utilizing four microsatellites markers. Palaeobotanical data were collected and combined with the genetic results in order to support the possibility that this species survived in northern refugia. Our study indicated that: (i) Balkan populations are the most divergent, which likely reflects their long-term in-situ existence, (ii) Western Alpine populations are genetically different from other European populations, which corresponds with palaeobotanical data, suggesting that this region served as a refugium for this species, (iii) the macrofossil data indicate that the Scandinavian and northeastern Polish populations are likely derived from the refugia located in northern latitudes, (iv) Western and Eastern Carpathian populations form separate groups, which indicate that both regions could serve as refugia. Clonality was an important factor in allowing grey alder to survive in northern regions during the last glaciation. However, this mode of reproduction has also influenced the population genetic structure, as we noted rather low level of gene diversity, HE = 0.386 and low allelic variability, A = 3.8, in this species.