Predispersal seed predation can be detrimental for any plant, but especially for rare plants. In this study, we examined the relationship of predispersal seed predation to different habitat types (i.e. open, semi shaded, and shaded), population size, and population density for Synthyris bullii, a rare Midwestern US endemic plant. In 2009, 2010, and 2011, a total of 18 populations were sampled across the range of Synthyris bullii. Fruit damage and predispersal seed predation were determined from up to 20 randomly collected infrutescences from each population. Predispersal seed predation had an impact on reproductive output and varied by habitat type. In addition, predispersal seed predation varied by population size and population density. Understanding the effects of predispersal seed predation on rare plants can be crucial for maintaining stable populations and developing better conservation and management strategies.