Resource sustainability requires a thorough understanding of the influence of forest management programs on the conservation of genetic diversity in tree populations. To observe how differences in forest management affect the genetic structure of Fagus orientalis Lipsky (oriental beech), we evaluated thirteen beech sites across Hyrcanian forests, based on six microsatellite loci. Significant differences between managed (mostly shelter wood system) and unmanaged populations was revealed. Inbreeding coefficient in managed populations was higher than unmanaged populations. A low, but significant, differentiation among all populations was found which reveals a clear geographic structure. Although the results indicate that the shelter wood system has minimum impact on the genetic diversity on a short term in oriental beech, but definitely inbreeding can increase in beech populations under intense management for long periods of time. According to these results, 4 populations from different part of Hyrcanian forests are suggested as potential in situ conservation sites.