Subgenus Nothofagus consists of five woody species that are present in diverse forest associations of temperate forests of Argentina and Chile. Given the variable conditions of the physical environment, structural and functional intraspecific variation with genetic basis is expected. The study of the gene pool of multiple populations of the different species at the regional scale using conserved nuclear and cytoplasm markers resolved the phylogenetic relationships within the subgenus and reconstructed their biogeographic history in Patagonia, respectively. Nuclear ITS sequences showed that N. pumilio diverged earlier and that N. antarctica is sister to the monophyletic group containing the three evergreens (N. betuloides, N. dombeyi, and N. nitida). Phylogeographic analyses based on sequences of chloroplast DNA allowed the reconstruction of ancient features of the Oligocene-Miocene landscape of Patagonia and showed paleohybridizations. The contemporaneous signal yielded by isozyme polymorphisms contributed to the analysis of spatial variation patterns such as the effect of the geographic range, the formation of clines and ecotypes, the genetic consequences of natural disturbances in relation to the predominant regeneration mode (sprouter and nonsprouter), and hybridization. Analysis on distinct habitat types inhabited by N. antarctica and experimental studies under common gardens and reciprocal transplants of N. pumilio at contrasting elevations showed genetic and plastic responses in ecophysiological and morphological characters. Taxa within subgenus Nothofagus are ancient lineages that have developed adaptations throughout their evolutionary history and therefore they may have the potential to respond to changes in climate.