Background The common primrose, Primula vulgaris, along with many other species of the Primulaceae, exhibits floral heteromorphy in which different individuals develop one of two possible forms of flower, known as pin and thrum. Both flower types are hermaphrodite and exhibit reciprocal positions of male and female reproductive structures, which together with a sporophytic incompatibility system, prevent self-pollination and promote out-crossing. The development of the two different forms of flower is controlled by a co-adapted linkage group of genes known as the S locus. ScopeHere progress towards identification and characterization of these genes is described to provide a molecular genetic explanation of the different floral characteristics that define heterostyly in Primula as observed and described by Charles Darwin. Previous work to identify and characterize developmental mutations linked to the P. vulgaris S locus, together with the isolation of S locus-linked genes and polymorphic DNA sequences markers, is summarized. The development of tools are described which will facilitate isolation and characterization of the S locus and its environs, including the creation of two expressed sequence tag libraries from pin and thrum flowers, as well as the construction and screening of two bacterial artificial chromosome (BAC) libraries containing thrum genomic DNA. Screening of these libraries with four S locus-linked sequences has enabled us to assemble four BAC contigs representing over 40 individual overlapping BAC clones which represent over 2·2 Mb of S locus-linked genomic sequence. PCR-based approaches for identification of the allelic origin of these BACs are described as well as identification of an additional 14 S locus-linked genes within BAC-end sequences. ConclusionsOn-going work to assemble the four S locus-linked contigs into one contiguous sequence spanning the S locus is outlined in preparation for sequence analysis and characterization of the genes located within this region. © The Author 2011. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved.