We investigated the structure and expression of three S-alleles of Petunia hybrida in self-incompatible varieties and in a pseudo-self-compatible line in which the self-incompatibility response is defective. Comparison of derived amino acid sequences from different gametophytic S-alleles revealed a pattern of sequence conservation and variability that was highly nonrandom. In self-incompatible varieties, petunia S-locus mRNA accumulates preferentially in styles during the transition from bud self-compatibility to self-incompatibility. S-Allele sequences homologous to the cloned S1 allele were present in a pseudo-self-compatible variety, and were expressed at levels indistinguishable from those observed in a self-incompatible line homozygous for the S1 allele. Taken together, our data indicate that (1) limited sequence differences may confer allelic specificity, (2) S-locus mRNAs accumulate in a precise organ-specific pattern during floral development, and (3) the ability to inhibit the growth of incompatible pollen tubes appears to require a threshold accumulation of the stylar gene product, along with the participation of as yet undefined pollen gene products.