North America, prairie and savanna remnants suffer from increased habitat degradation and structural changes (e.g., woody encroachment). Plant populations in remnant habitats may be threatened over time as a result of this degradation. Past studies have explored plant responses to such changes by focusing primarily on vegetative characteristics rather than reproductive ones. Our research uses a rare Midwestern endemic, Synthyris bullii, to determine if the morphology of reproductive structures is associated with habitat quality. Study populations were visited and categorized according to the level of observed woody encroachment: shaded, semishaded, and open. From each population, 20 individuals were selected to measure inflorescence size (i.e., inflorescence height and flower number) and flower size (e.g., lengths of petals, stamens, carpels). Data were explored by canonical discriminant analysis to determine if traits were associated with particular habitat types and then analyzed by MANOVA and univariate ANOVAs to determine differences in traits among habitats. Results showed that floral morphometrics differed in open and shaded habitats, though semishaded habitats did not generally differ from the other two categories. Specifically, shaded habitats produced smaller inflorescences (e.g., fewer flowers) with larger flowers (e.g., increased lengths of petals and carpels), while the inverse pattern was observed in open habitats. Although we initially predicted consistent reductions in size across reproductive traits, we found instead inverse size patterns at the inflorescence level versus the flower level in different habitats. Our study highlights the impact of habitat changes that could ultimately affect the reproductive success of S. bullii and contribute to its decline.