Premise of the study: Knowledge on the range-wide distribution of genetic structure and diversity is required to facilitate the understanding of historical tree migration and for predicting responses to current climate change. With respect to post-glacial migration patterns known from the northern hemisphere, we tested the prediction that the southernmost populations of a subtropical tree line species have lower within-population genetic diversity and higher genetic differentiation than the central and northernmost populations. Methods: We used AFLP to assess the genetic structure of 18 populations of the wind-pollinated Polylepis australis (Rosaceae) sampled over its entire distributional range in three Argentinean high mountain regions. Genetic diversity was calculated as a percentage of polymorphic bands (P) and Nei's expected heterozygosity (He); genetic differentiation was assessed using AMOVA, Φ _ST - statistics, and Bayesian cluster analysis. Key results: Contrary to our expectations, the northernmost Polylepis australis stands had lower within-population genetic diversity and higher genetic differentiation than the central and southernmost stands. Populations grouped into two major clusters, the first containing the southern populations and four central populations and the second containing the northern and one central population. Conclusions: Patterns of Polylepis australis genetic structure and diversity differ from historical migration scenarios observed for the northern hemisphere. The decline in genetic diversity toward the north may point to an equatorward migration following past climatic changes. Populations within the south and central part appear to be connected by effective long-distance pollination while gene flow in the northern part is probably hampered by geographic isolation.