We isolated 18 cDNA candidates that were expected to encode parts of the self-incompatibility-associated RNase of Lycopersicon peruvianum PI 126441 (S11a-plant) from a style cDNA library. Polymerase chain reaction was used with oligonucleotides derived from conserved amino acid sequences of RNases from fungi and S-associated RNases in other species of Solanaceae. Two of these clones (both do not have full length sequences) gave 826-bp and 730-bp sequences, and they had the same open reading frame, named ORF-1. Comparison of the deduced amino acid sequence of ORF-1 with S-associated RNase of other Solanaceous plants showed a high degree of similarity. mRNA encoding this ORF-1 was about 1000 bases long and detected only in the style tissue by Northern analysis. Using one of the cDNA clones as a probe, we detected sequence variability among three different S-genotypes of randomly chosen wild-type tomatoes by Southern analysis. From these results, it was concluded that ORF-1 encodes the self-incompatibility associated S-glycoprotein of L. peruvianum PI 126441 (S11a-plant).