Allelic polymorphism at the S locus that determines the gametophytic self-incompatibility (GSI) system in the pistil predates speciation. Understanding the evolution of a GSI system therefore requires knowledge of how lineage sorting and interspecific phylogenetic relationship affect S allele polymorphism. In searching for patterns of lineage sorting among species of various phylogenetic relationships, 22 S-alleles from 34 genets randomly taken at three Tennessee sites from a newly known GSI species Physalis longifolia were sequenced. Analyses of these data along with the previous sequences of three solanaceous species indicate that much of the combined allelic genealogy may be explained by lineage sorting and phylogenetic relationship. Using the mean terminal branch lengths of trans-specific alleles on the allelic genealogy to infer phylogenetic relationship among species, P. longifolia was found to be more closely related to P. cinerascens than to P. crassifolia. Nonetheless, the distribution of terminal branch lengths of P. longifolia was more similar to that of P. crassifolia than to that of P. cinerascens, suggesting phylogenetic relationship may have little effect on species-specific polymorphism. Similar habitat and growth characters, yet contrasting S-polymorphism, between P. longifolia and P. cinerascens also reject previous hypotheses that habitat and growth characters are the major factors responsible for interspecific differences in S-polymorphism. A likely scenario is that species-specific S-polymorphism is based on lineage sorting whose effect is further modified by species age and historical changes in population parameters.