To our knowledge, this is the first study designed to determine the genetic factors of disease resistance to beech bark disease (BBD) with genome scan analysis in American beech tree. The results presented identified four highly significant markers associated with a single locus located on chromosome (Chr) 5. All four loci were localized to the same contig within a single gene (Mt), that encodes for Fagus sylvatica mRNA for metallothionein-like protein (metal ion binding). Once a reference genome sequence is available, it will be possible to gain more insight into functional annotation of the four SNPs and determine the exact number of genes associated to BBD.