<p>European larch (<i>Larix decidua</i> Mill.) is a common deciduous conifer tree species naturally occurring in the Alps and in scattered populations in Central-Eastern Europe, including the Jeseníky region (NE Czechia). It is commonly planted in forests and especially some of its traditionally described regional types are highly valued in forestry for outstanding form and wood properties. Here we present the results of the first research to date focused on the genetic structure of a larger number of larch populations from the Jeseníky region using analysis of nuclear DNA microsatellite markers in the context of the variability throughout the whole range of the species. The region is traditionally considered to be a part of the native distribution range of larch and a specific local type of larch, called ‘Sudety’ or ‘Jeseníky’ type, has been described there. We confirm a common presence of the ‘Sudety’ type in a form of a genetic lineage closely related to larch populations from northern Carpathians and lowlands of Poland. However, we found notable levels of artificial admixture of genetic material from the Alps in many of the populations, including the populations specifically protected to preserve the local type of larch. The admixture is either low or absent in the core protected populations but in the periphery, including some of the protected areas, and commonly managed forests, the Alpine genotypes can reach up to 50% or even dominate. Our research proves how important detailed investigation of population genetic structure can be for practical nature conservation and forest management even in the case of very common species.</p>