Forest fragmentation and introduced pathogens are negatively impacting trees and forests globally, including the Carolinian forest of southern Ontario, Canada. Multiple species at risk live in this threatened but biodiverse forest, including the endangered Cornus florida (eastern flowering dogwood), which is now limited to fragmented woodlots, and has been decimated by the introduced fungal pathogen Discula destructiva (dogwood anthracnose). Ongoing management of C. florida in Canada is challenged by multiple knowledge gaps, two of which we aimed to address in this study. We first evaluated the association between anthracnose disease prevalence and a suite of ecological and environmental variables across 21 sites. Across our sites, larger trees tended to have the highest disease incidence, and trees on shallow slopes had the most crown dieback. We then quantified genetic diversity and gene flow, and found that genetic structure has not been substantially impacted by habitat fragmentation, although dispersal typically covers short distances. However, genetic diversity is relatively low in smaller populations and in younger trees. Localized dispersal and eroding genetic diversity may limit future adaptation and hence exacerbate population declines. We recommend that managers prioritize plantings in small populations, avoid shallow slopes, and track younger trees to evaluate age-related mortality. [ABSTRACT FROM AUTHOR]