Global declines in biodiversity create an urgent need to address the impact of infectious disease in the small and fragmented populations that characterize threatened species. However, the paucity of empirical data provides little ability to predict whether disease generally accelerates threatened species towards extinction or becomes less important as populations decline. This study tests whether plant species threatened with extinction exhibit lower disease frequencies and lower overall parasite species richness while also experimentally testing for the effect of physiological disease resistance. Herbarium surveys of the genus Silene revealed that anther-smut disease was significantly less frequent in threatened species than non-threatened species, and this effect was not constrained by the host phylogeny or by physiological resistance. Moreover, analysis across a much broader range of plants (using US Federal designations) revealed that species with endangered status had significantly lower species richness of fungal pathogens than closely-related, non-endangered species. These results support the role of host ecology, rather than physiological resistance or phylogeny, in determining overall lower incidences and diversity of diseases in plant species threatened by extinction. Low disease incidence accompanied by susceptibility in threatened species may result from selection against costly resistance genes in the absence of disease.