The self-incompatibility (S) locus of flowering plants offers an example of extreme polymorphism maintained by balancing selection. Estimates of recent and long-term effective population size (N-e) were determined for two solanaceous species by examination of S-allele diversity. Estimates of recent N-e in two solanaceous species differed by an order of magnitude, consistent with difference in the species’ ecology. In one species, the evidence was consistent with historical population restriction despite a large recent N-e. In the other, no severe bottleneck was indicated over millions of years. Bottlenecks are integral to founder-event speciation, and loci that are subject to balancing selection can be used to evaluate the frequency of this mode of speciation.