The simple codominant expression of the alleles at the self-incompatibility locus ( S) of Solanaceae and their extraordinary spectrum of sequence diversity present an ideal case for understanding the molecular forces that shape the sequence polymorphism of genes involved in recognition reactions. Here, with unprecedented conspecific sequences of 33 Physalis longifolia S alleles, including 27 of their single introns, the tempo-spatial nucleotide substitution patterns were first detailed for the S locus and analyzed in genealogical time scales. Three major genealogical clades of the 33 P. longifolia S alleles were used to divide the genealogical time into the within-clade and the between-clade periods. During the within-clade period, the average nonsynonymous substitution rate was 50% higher than the intron substitution rate but the opposite trend emerged for the between-clade period. A new and simple method developed here was utilized to estimate the selection intensity in the coding regions. The magnitudes and the distribution of these estimates, in conjunction with the spatial substitution pattern among closely related S sequences, revealed an initial short-term action of strong positive selection and a continuous but weaker action of negative selection brought by functional/structural constraints on the S alleles. The two modes of selection can significantly modify the branch lengths of an S genealogy and may be ubiquitous to recognition systems.