The spatial pattern of chloroplast DNA (cpDNA) variation in Quercus robur, Quercus petraea and Quercus pubescens was studied in 1036 trees from 181 locations throughout the Swiss Alps and adjacent regions in order to gain a deeper insight into the postglacial history of these species. A total of ten different cpDNA types (haplotypes) were identified, six of which are described for the first time. The genetic variation was mainly found between collection sites (G_ST=0.881). Spatial autocorrelation indicated that the two dominant haplotypes had a structured, non-random distribution. The spatial pattern of these two haplotypes, which are associated with different ice-age refugia, reveals: (1) that oaks did not immigrate into regions of the Swiss Alps together, rather they immigrated separately in space and/or time, and (2) that the spatial mixing of haplotypes as a consequence of seed dispersal was low. Furthermore, the geographic distribution of the haplotypes suggests that the Alps only partially blocked the re-colonisation of oaks: Quercus species, which originated after range expansion from a refugium in Italy, have most likely crossed the Swiss Alps. Previously proposed postglacial migration pathways are reviewed and possible re-colonisation routes are discussed.