Disease epidemiology has rarely been examined in natural plant‐pathogen systems exhibiting obligate alteration of host species. We quantified rust infection in populations of jewelweed; its effect on host mating system, potential biotic and abiotic correlates of infection; and spatial patterns within populations. Jewelweed (Impatiens capensis) is a woodland annual that can become infected with the heteroecious rust, Puccinia recondita, whose alternate hosts are often grasses. It produces dimorphic self‐pollinated cleistogamous (CL) flowers and open‐pollinated chasmogamous (CH) flowers. Infected plants may have fewer resources, so we predicted a decrease in CH flowering relative to that of uninfected plants. Infection occurred early in the growing season and disappeared by midsummer, although plants continued to grow and flower until the frost. We found no clustering of infection within populations. Infection prevalence did not vary among sites in 2005, but one site had more disease in 2004 than in 2005. R...