A number of insects and diseases cause significant loss to forest productivity. Most of the current operational strategies for insect and disease control rely on classical breeding methods to develop populations enriched for resistance . With emergence of genomics-based approaches, such as genome-wide association studies (GWAS) and genomic selection (GS), a broader range of applications is now available for plant breeding and genetic research [55, 56]. In Fagus, mapping populations have been developed to discover QTLs for traits correlated to BBD. The tree improvement program included crosses to study inheritance of resistance to Cryptococcus fagisuga (see [19, 57]). However, association mapping like GWAS for QTLs underlying disease resistance to the BBD, has not been previously reported. In the present study, we used a GWAS mapping approach and a SNP linkage map to identify candidate resistance genes. To confirm the SNPs identified are truly associated with the scale-resistant trait, replication of this GWAS study is necessary, using independent case-control data from the initial population of unrelated individuals (see [58, 59]).