The last glaciation was one of the most severe of the Pleistocene epoch. The development of the Scandinavian ice sheet forced many species to reduce their ranges to areas with favourable climatic conditions. Most European species survived the Last Glacial Maximum in refugia in southern parts of Europe. Cold-tolerant species, such as birch trees and shrubs, could also inhabit western, eastern or central Europe. After climate warming, Holocene recolonisation began. This paper presents a comparative analysis of the genetic variation of four European Betula species to reconstruct their glacial and postglacial histories. Two chloroplast DNA haplotypes dominate within the ranges of all birch species, one haplotype is the most common in western and northwestern Europe, the second haplotype occurs mainly in the eastern and southeastern parts of the continent. This finding suggests that birches have recolonised Europe from the western and the eastern refugia, respectively. Most of Europe was likely populated from higher latitude refugia because there was no evidence of isolation by distance and weak genetic structures were detected. Similar patterns of haplotype distributions within Betula ranges indicate that postglacial recolonisation may be disturbed by interspecies hybridisation.