In taxa with few diagnostic characters, highly variable populations pose a major challenge to delimiting species. This is especially true in Dodecatheon (Primulaceae), which has a notoriously complex taxonomic history. Previous biosystematic studies of Dodecatheon in southern Illinois support the recognition of two species: D. frenchii, a diploid sandstone cliff endemic, and D. meadia, a widespread tetraploid. However, only one morphological character distinguishes them and some experimental evidence suggests that this character may be environmentally induced. Furthermore, authors have disagreed about the nature of morphologically intergrading populations. In this study, we document patterns of variation for fruit and seed characters among populations in southern Illinois, including one atypical, morphologically intergrading population. Different seed shapes help distinguish these taxa, both in southern Illinois and across their larger ranges. We also show that the intergrading population is significantly more variable than others, and describe the occurrence of such populations in other regions where these two taxa co-occur. These two results suggest that localized hybridization between these species may contribute to their complex taxonomic history.