Dominant self-incompatibility (SI) haplotypes, introgressed from 'Brassica rapa', have been used at the University of Guelph to produce hybrid 'B. napus' canola. In this study, PCR markers were developed to amplify specific alleles of the S locus glycoprotein gene of SI haplotypes from 'B. napus' genomic DNA. The roles of these markers in hybridity assessment, as tools within the SI 'B. napus ' breeding program, and in studies of the expression of SI in ' B. napus' were considered. Use of these markers for hybridity assessment in 'B. napus', which has two independently segregating S loci, has implications for hybrid design. Analysis of segregating F2 populations containing one or two SI haplotypes revealed: (1) evidence of introgression of a SI haplotype into the homeologous S locus; (2) the presence of modifier loci affecting the expression of SI phenotypes; and (3) a gametophytic influence on transmission of male gametes in crosses.