Aster furcatus is a rare species with extremely limited genetic variation at isozyme loci. We utilized crossing experiments and seed set data obtained from natural populations to verify that there is also little allelic variation at the self‐incompatibility (S) locus. Seed set in several populations was limited by a low number of S‐alleles. Associated with a low number of S‐alleles in populations was the dissolution of the incompatibility system, manifest by individual variation in self‐compatibility, and by complex dominance relationships among S‐alleles. Plant self‐compatibility was correlated with mean number of ovules per inflorescence. Thus, self‐compatibility appeared to be under partial environmental influence. Computer simulations revealed that the shapes of seed set distribution curves of modeled self‐incompatible plant populations depend on the number of incompatibility alleles in the populations. By varying the number of S‐alleles in modeled populations, we generated seed set distribution curves similar to those of natural populations. Genetic bottlenecks reduce the number of S‐alleles and the proportion of compatible matings in populations of multiallelic self‐incompatible species. Self‐compatible genotypes are at a selective advantage in populations that lack a sufficient number of S‐alleles to produce compatible crosses. Aster furcatus appears to be evolving self‐compatibility as a result of bottleneck‐induced losses of S‐alleles.