Fungal and oomycete plant pathogens are believed to be an important mechanism maintaining tree species diversity via control of seedling growth and survival. Despite this, relatively little is known about the role of pathogens in temperate forests. We characterized the fungal and oomycete pathogens causing seedling mortality for fourteen southeastern U.S. forest tree species, and we tested a classic hypothesis predicting that host-specific pathogens drive spatial patterns of seedling recruitment. Planted seedlings were surveyed weekly for mortality over one growing season, and dead or dying seedlings were assayed for pathogens. We used culture-based methods to isolate fungi and oomycetes, and DNA sequencing to identify them to the genus or species level. Germination and survival rates of tree species varied between species, sites, and in time. Oomycetes could be cultured from approximately 10% of collected seedlings; potentially pathogenic fungi could be cultured from 73%. Eighty-four morphotypes of ascomycete fungi have been delimited; of these, twenty-nine are represented by a single culture. Some of the most common fungal morphotypes are tentatively identified as belonging to the genera Colletotrichum and Nectria, which contain many known pathogens. Colletotrichum collections are widespread between species and sites; Nectria collections are found in a higher proportion at one location, but across several species. Oomycete cultures include at least two strains of Pythium and Phytophthora cinnamomi. Approximately two-thirds of oomycete cultures were found on Quercus seedlings. Pathogenic fungi and oomycetes are common in this system, but the effect of pathogens on tree diversity depends strongly on pathogen identity.