Developing "climate smart forestry" (CSF) indicators in mountain forest regions requires collection and evaluation of local data and their attributes. Genetic resources are listed among the core indicators for forest biological diversity. This study is a report on the evaluation of the standing genetic diversity within and across 12 pure beech stands (Fagus sylvatica L.) established within the CLIMO (CLImate Smart Forestry in MOuntain Regions) project, using nuclear microsatellite markers. The sampling sites were set along the species' distribution range, including the Balkan region and extending towards the Iberian Peninsula. Cores or leaves from 20 to 23 old, mature trees per plot were sampled for DNA analysis. Genetic diversity indices were high across the range (H-E = 0.74-0.81) with the highest in the Bosnian Mountains. Genetic divergence increased significantly with the geographical distance (Mantel test: r = 0.81, p < 0.001). Most of the stands exhibited an excess of heterozygotes, with the highest value at the Hungarian site (H-O/H-E = 1.177), where beech persists close to the eastern xeric limit of the species' distribution. STRUCTURE revealed within-region differentiation in the Balkan Peninsula, where the Bulgarian stand was the most outstanding. The genetic parameters of each stand could be assessed as a resource for CSF indicators interpreted especially at the local level.