Aextoxicon punctatum, the only representative of the family Aextoxicaceae, is a tree species endemic to temperate forests of western South America. This species exhibits a disjunct distribution pattern, with few isolated populations occurring on coastal hilltops of the Chilean semi-arid zone (SAZ), 30–32°S; small populations mixed with sclerophyllous forest in some gorges of the central Chilean Mediterranean coastal range (MCR), 32–39°S; more continuous forests extended along the southern temperate coastal range (TCR), 39–43°S; and fragmented populations eastward in the south temperate central depression and Andean foothills (TAF), 39–41°S. This geographic disjunction is the result of climatic and tectonic changes that took place in southern South America since the late Tertiary, leading to the isolation of forest fragments in the SAZ from the rest of the distribution. According to palynological evidence, populations of TCR and TAF originated from postglacial population expansions from refuges located on the coastal range, north of 40°S. We examined how the present genetic structure and diversity of Aextoxicon populations in Chile reflects this biogeographic history. Random amplified polymorphic DNA (RAPD) markers were used to characterise genetic differences within and among 16 populations of this species throughout its natural range. AMOVA and UPGMA analysis showed high genetic differentiation between the geographically closer SAZ and MCR populations, suggesting a long history of restricted genetic exchange between populations in these two zones. Estimates of Shannon’s genetic diversity and percentage polymorphism were relatively low compared with other southern temperate forest trees (mainly conifers) that were less affected by the glaciations. Positive correlations between genetic and geographic distances were found for TCR but not for TAF populations, suggesting earlier postglacial population expansion southwards along the TCR and more recent eastward migration from coastal locations to TAF during the Holocene.