Technical Abstract: Canopy disturbances such as windthrow events have obvious impacts on forest structure and composition aboveground, but changes in soil microbial communities and the consequences of these changes are less understood. We characterized the densities of a soil-borne pathogenic oomycete (Pythium) and a common saprotrophic zygomycete (Mortierella) in nine pairs of forest gaps created by windthrows and adjacent forest understories. We determined the levels of Pythium necessary to cause disease by performing pathogenicity experiments using two Pythium species, a range of Pythium densities, and two common tree species (Acer rubrum and Prunus serotina) from the study sites. Three years post-disturbance, densities of Pythium and Mortierella remained suppressed in soil from forest gaps compared to levels in intact forest understories. Expression of disease symptoms increased with increasing inoculum density for seedlings of P. serotina with each Pythium spp. having a similar effect on this species. Conversely, A. rubrum appeared resistant to Pythium. These results suggest that Pythium densities in the field are sufficient to cause disease and have the potential to affect establishment of susceptible species like P. serotina. Because early seral environments have lower pathogen loads, susceptible species are more likely to become established in those settings than in late-seral forests. Forest disturbances that alter the disease landscape may provide an additional mechanism for explaining succession of temperate forests in addition to the shade-tolerance paradigm.