Silver fir and European beech are keystone forest tree species that are under pressure in a large part of their distribution because of climate change. Their south-eastern limits are very important since they: (a) face immediate climatic change-related challenges as a combination of increased temperatures and drought are expected, (b) Species Distribution Models question their persistence in the long term, and (c) contain germplasm well adapted to conditions similar to those expected in central Europe by the end of the century. Their most south-eastern populations were sampled (30 trees per population; Mt. Pinovo and Mt. Oxia, Greece, respectively), and genetic variation was assessed using SSRs. Observed (Ho) and expected heterozygosity (He), as well as allelic richness (AR) were calculated and results were compared against populations throughout the species’ natural range. Results for silver fir (Ho=0.452, He=0.530), indicate values generally lower than those of populations from the rest of its distribution such as in Central Europe, the Balkans and the southwestern edge and eastern range limits. Only some populations from Spain and Italy were detected to have lower values than the population of this study. Allelic richness (AR=6.29), was found higher than Italian populations, but lower than central and northern Balkan populations. In European beech (Ho= 0.732, He=0.753), values were higher than those of German and Czech populations, comparable (or lower in some cases) than populations from France, Spain and Italy, but lower than populations from elsewhere in Central Europe (e.g. Poland). Allelic richness (AR=6.63), was higher than France and comparable to the values of populations from the rest of species European populations.