Primula species provide possibly the best known examples of heteromorphic flower development and this breeding system has attracted considerable attention, including that of Charles Darwin. However, despite considerable recent advances in molecular genetics, nothing is known about the molecular basis of floral heteromorphy. The first molecular marker for the Primula S-locus is reported here. This DNA sequence was identified by random amplification of polymorphic DNA (RAPD)-PCR, further defined as a sequence characterized amplified region (SCAR) marker, and subsequently shown to correspond to a restriction fragment length polymorphism (RFLP) that is linked to the thrum allele of the Primula S-locus. The sequence of 8.8 kb of genomic DNA encompassing this thrum-specific RFLP is presented. Analysis of this DNA reveals a highly repetitive sequence structure similar to that found at the S-locus in other species; it also contains sequences similar to elements of a Gypsy-like retrotransposon. The identification of a specific DNA sequence associated with the thrum allele of the Primula S-locus provides the first molecular probe with which to investigate the molecular basis of heteromorphic flower development in Primula.