Chloroplast DNA polymorphisms were analysed to infer the post-glacial history of Nothofagus nervosa (Phil.) Dim. et Mil., a species endemic to South American Temperate Forests. Two hypotheses were postulated to explain the current distribution of the species in relation to the refugia proposed after palynological studies and the time elapsed since Last Glacial Maximum. If refugia were located only in the Coastal Mountains, as pollen records suggests, long-distance dispersal events should be invoked to explain the current occurrence of the species in southern latitudes. The alternative hypothesis is the existence of cryptic refugia in southern latitudes. A total of 26 populations covering the entire geographical range of the species in Chile and Argentina were analysed through PCR-RFLP. Five haplotypes were identified, and a very low intrapopulation variation was observed together with a high gene differentiation (GST=0.93). The haplotypes showed a highly structured geographic distribution, separating populations located in the Pacific Coastal Mountains from those coming from the easterly located Andes Mountains. Moreover, among the populations of the Andes Mountains a north-south variation in the distribution of haplotypes was found. The results strongly suggest the persistence of the species in several ice-age refugia. The possible location of such refugia is discussed in combination with the available palynological data.