Lagunas de Epulauquen forests (36°49'S; 71°04'W) have been considered the northernmost population of Nothofagus obliqua in Argentina. Recently, however, its taxonomic status has been questioned due to its morphological, architectural and genetic distinctiveness. The convergence of migratory routes and hybridization with Nothofagus alpina are the two main hypotheses proposed to explain the distinctiveness of this population. Despite its unique characteristics, no evaluation of its putative origin has been carried out. In order to test the hypothesis of hybridization we analyzed nuclear Adh and ITS fragment sequences together with 12 nuclear microsatellites. These nuclear regions were selected based on their previously reported divergence between N. obliqua and N. alpina. The survey was conducted in 12 individuals from Lagunas de Epulauquen, and individuals from N. obliqua (8), N. alpina (1), N. macrocarpa (2), N. glauca (4) and N. leonii (2). By combining a phylogenetic analysis with a principal coordinate analysis of microsatellite data, we showed that Lagunas de Epulauquen individuals were closely related to other N. obliqua individuals, while hybridization with N. alpina was not detected. Our results indicate that hybridization processes could be discarded as the origin of the Lagunas de Epulauquen distinctiveness. The hypothesis of the convergence of two N. obliqua migratory routes at this latitude was reinforced based on detected patterns of genetic diversity. Notwithstanding, its high geographical isolation seems to be also a key evolutionary factor to explain the distinctiveness of this population. Lagunas de Epulauquen population could be therefore included within Argentinean N. obliqua domestication and conservation programs.