Several field trials showed some beech trees remain after infestations that appear to be naturally resistant to BBD, usually clustered in small groups [16, 17]. About 1% of American beech trees remain disease free in forests long-affected by BBD . There have been a small number of studies to understand the genetics of resistance of American beech to BBD [17–20]. Several studies have been conducted using molecular markers such as isozymes, RAPD (random amplified polymorphic DNA), AFLP (amplified fragment length polymorphism) and SSRs (simple sequence repeat) to differentiate between resistant and susceptible individuals and identify markers correlated with resistance, evaluate spatial and population genetic structure, and perform parentage analysis [19, 21–24]. Although genetic marker studies enhanced the efforts to clarify modes of inheritance, no markers have been discovered that correlate with resistance. To estimate heritability, resistance to the beech scale insect, the artificial infestation technique developed by Houston , was used to test parent trees and their full and half-sibling progeny for resistance . Individuals were classified as susceptible if five or more scale insects were present on the bark surface 1 year after scale insect eggs were affixed to the test tree. Low levels of resistance were found in families with only one resistant parent and a higher proportion of resistant progeny were only observed in families where both parent trees were resistant, confirming that resistance to beech scale insect is a heritable trait [19, 24]. Current screening for resistance aims to increase the proportion of resistant trees and remove the susceptible trees for breeding purposes. These results formed the basis of a regional breeding program for BBD-resistant American beech [5, 25]. Identification of genetic markers associated with the resistance phenotype could potentially accelerate breeding efforts and reduce costs through the implementation of indirect selection methods, reducing the need for the costly, time consuming and labor intensive methods currently used to test trees for resistance to the scale insect.