Sporophytic self-incompatibility (SSI) in Ipomoea trifida is controlled by a single, multi-allelic S locus. In previous map-based cloning studies of the SSI locus (S locus), we sequenced genomic regions covering the S loci of the S 1 and S 10 haplotypes. We identified a highly divergent region of about 50 kb in the S 1 haplotype and suggested that the Ipomoea S locus genes are located within this genomic region. In the present study, we used the sequenced DNA fragments as probes for RNA blot analyses and found 14 genes that were expressed in tissues of S 1 haplotype plants. Six of the genes were located within the S haplotypespecific divergent region (SDR), and were specifically expressed either in female or male tissues. RT-PCR analysis confirmed that three genes, named here SE1, SE2 and SEA, showed stigma-specific expression, and that one gene, named here AB2, exhibited antherspecific expression. Expression of these genes was developmentally regulated and was detected at high levels in young flower buds before anthesis. In situ hybridization also showed that AB2 was expressed in the tapetal cells of the anther. Analyses of cDNA clones derived from these stigma-or anther-specific genes revealed that they exhibited high levels of sequence polymorphism in three S haplotypes, although we also detected several transcripts produced by alternative splicing of the SE2, SEA, and AB2 gene products. The present study suggests that the highly polymorphic genes SE1, SE2 and SEA that are expressed in the stigma and AB2 that is expressed in the anther are candidates encoding pistil and pollen determinants, respectively, in the SSI system of Ipomoea.