Abstract
Variation in the chloroplast genome of Ilex aquifolium (English holly), a dioecious evergreen tree native to south, west and central Europe, was analysed using polymerase chain reaction–restriction fragment length polymorphisms (PCR‐RFLPs) and microsatellites. Differentiation between populations was high ( G ST = 0.595) and evidence for phylogeographical structure was detected ( N ST = 0.697, significantly higher than G ST ). Two chloroplast lineages were inferred originating from putative glacial refugia in southern Europe (Iberia, Italy and possibly the Balkans). The G ST value was higher than reported for endozoochorous hermaphrodite species and for anemochorous dioecious species investigated over a similar geographical scale. It appears that dioecy has contributed to strong differentiation between refugia and that this has been maintained following postglacial recolonization as a result of limited seed flow. Palynological records for I. aquifolium are poor, thus these results give an important insight into patterns of glacial isolation and postglacial recolonization of this species.