In homomorphic plant self-incompatibility (SI) systems, large numbers of alleles may be maintained at a single Mendelian locus. Most estimators of the number of alleles present in natural populations are designed for gametophytic self-incompatibility systems (GSI) in which the recognition phenotype of the pollen is determined by its own haploid genotype. In sporophytic systems (SSI), the recognition phenotype of the pollen is determined by the diploid genotype of its parent, and dominance differs among alleles. We describe research aimed at estimates of S-allele numbers in a natural population of Arabidopsis lyrata (Brassicaceae), whose SSI system has recently been described. Using a combination of pollination studies and PCR-based identification of alleles at a locus equivalent to the Brassica SRK gene, we identified and sequenced 11 putative alleles in a sample of 20 individuals from different maternal seed sets. The pollination results indicate that we have not amplified all alleles that must be present. Extensive partial incompatibility, nonreciprocal compatibility differences, and evidence of weakened expression of SI in some genotypes, prevent us from determining the exact number of missing alleles based only on cross-pollination data. Although we show that none of the theoretical models currently proposed is completely appropriate for estimating the number of alleles in this system, we estimate that there are between 13 and 16 different S-alleles in our sample, probably between 16 and 25 alleles in the population, and discuss the relative frequency of alleles in relation to dominance.