AbstractAim  A multiple glacial refugia hypothesis for Mediterranean plant species was tested with the evergreen Quercus complex (Quercus suber L., Quercus ilex L. and Quercus coccifera L.) from the Iberian Peninsula, using molecular and palaeobotanical data.Location  The Iberian Peninsula, which is an ecologically and physiographically complex area located on the western edge of the Mediterranean Basin.Methods  We sampled 1522 individuals from 164 populations of Q. suber, Q. ilex and Q. coccifera. A review of the recent literature on fossil pollen and charcoal records and a nested clade analysis on chloroplast DNA polymerase chain reaction‐restriction fragment length polymorphism was carried out to infer demographic and historical processes.Results  The analysis indicates at least one glacial refugium for Q. suber in south‐western Iberia. Extensive introgression of Q. suber with Q. ilex indicates several potential refugia in eastern Iberia. Past fragmentation was followed by a restricted range flow/range expansion, suggesting multiple refugia for Q. ilex–Q. coccifera elsewhere in central and northern Iberia and multiple areas of secondary contact. This finding is consistent with fossil records.Main conclusions  The predicted multiple refugia during glacial periods indicates the existence of secondary post‐glaciation contact areas. These areas contained complex diversity patterns resulting mainly from range expansions followed by isolation by distance. To a lesser degree, traces of restricted and long‐distance dispersal were also found.