Queen-of-the-prairie, Filipendula rubra (Rosaceae), is a perennial, rhizomatous herb restricted to calcareous fens, spring seeps, and wet prairies, and is distributed in the northcentral United States from Iowa to New York. Because of the scarcity of adequate habitat, F. rubra is a rare and endangered species in several states. At Botkin Fen and other fens in Missouri, F. rubra possesses limited sexual reproduction. A study was conducted to determine causal mechanisms of its limited seed production that may be barriers to establishing this rare and endangered species in other fens in Missouri. A genetic-ecological hypothesis was supported. F. rubra was found to be self-incompatible. At Botkin Fen, most inflorescences produced very few seeds because most (85.4%) belonged to a single clone. Pollinators (Lassioglossum sp.) had a high probability of transporting pollen with the same self-incompatibility alleles. A few genetically different clones did produce significant quantities of seed. However, this seed, with its significant pool of genetic variability, was not recruited into the population. Apparently, competition from the dense sedges and grasses prevented the establishment of new seedlings.