Armillaria root diseases are among the most damaging and broadly distributed group of forest diseases in the world (Lockman et al. in press). Armillaria root disease is typically more severe in highly susceptible tree species and in trees that are maladapted due to rapidly changing climatic conditions (Ayres and Lombardero 2000, Kliejunas et al. 2009, Sturrock et al. 2011). Unfortunately, Armillaria root disease is notoriously difficult to manage in forests. Because Armillaria root disease impacts are dependent on complex ecological interactions among the host, soil microbial community, and environment, we propose the development of metagenetic tools to examine soil interactions that suppress (or enhance) Armillaria root disease. Tools to identify these interactions are paramount to develop effective management approaches for Armillaria root disease.