Non-indigenous pathogenic fungi increasingly threaten North American tree species. Ecosystems may be fundamentally changed when abundant tree species are functionally eliminated, as occurred with American chestnut (Castanea dentata (Marsh.) Borkh.). Conversely, changes may be more subtle but still significant and long lasting when populations are lost, or all trees in the larger size classes are killed. Proposed approaches for characterizing the magnitude of ecological impacts use characteristics of both the non-indigenous pathogen and the host species. Impacts are most significant when highly successful invading pathogens attack foundation species, setting in motion a long-lasting cascade of effects on the host and associated species. Such impacts have generally not been well documented at the ecosystem level. Several North American forest tree species have been functionally eliminated or severely reduced by non-indigenous pathogens. Historical invasions, such as that of chestnut blight (Cryphonectria parasitica (Murr.) Bar), caused very significant ecological impacts that will never be completely understood because of lack of quantitative data. Beech bark disease, caused by a combination of an introduced scale insect (Cryptococcus fagisuga Lindinger) and a fungus (Neonectria faginata (Lohman et al.) Castl. & Rossman), is still advancing and provides opportunities for studying ecosystem-level impacts when a major tree species is removed or markedly reduced in abundance from the overstorey. Butternut canker, caused by the fungus, Sirococcus clavigignenti-juglandacearum N.B. Nair, Kostichka & Kuntz, has spread throughout the host range, endangering species’ survival. Other non-indigenous invasive fungi such as Cronartium ribicola J.C. Fisch and Phytophthora lateralis Tucker & Milbrath continue to move into new populations, causing high mortality and associated restructuring of these ecosystems. Global trade and environmental change trends will ensure new challenges by non-indigenous fungal pathogens, presenting an urgent need for improved understanding of long-term impacts across ecological systems.