Rye inbred lines segregating at the S-locus and homozygous at the Z-locus were investigated by PCR with primers derived from Brassica SLG-sequences. After denaturing gradient gel electrophoresis (DGGE), a 280 bp PCR-fragment displays a polymorphism perfectly correlated to the underlying S-genotypes. This is the first report on S-related DNA polymorphism in a bifactorial self-incompatibility system of the Poaceae.