The A mating type factor of the hymenomycete fungus Coprinus cinereus is a multi-allelic gene complex that controls mating compatibility and sexual development. It contains up to four pairs of specificity genes, the a, b, c, and d gene-pairs. Each gene-pair codes for two homeodomain transcription factors with distinct classes of homeodomain motifs. Mating compatibility between the A42 and A6 factors depends solely on the different alleles of the b gene-pair, b1-1 and b2-1 in A42 and b1-3 and b2-3 in A6. The b1-3 and b2-3 genes of A6 were isolated and the complete DNA sequences of genomic and cDNA clones were determined. Construction of chimeric genes using the A42 and A6 b genes identified the N-terminal regions of the A proteins as being responsible for allele specificity. Analysis of protein-protein interactions showed that b1 and b2 proteins from different alleles of the same gene-pair can dimerise, whereas proteins from the same allele pair can not. It was shown that a region of 90 amino acids at the N-terminus of the b2-3 protein is sufficient for dimerisation with b1-1. This region is predicted to contain an amphipathic helix. A comparison with the equivalent region in the b2-1 protein identifies a similar helix. This suggests that a compatible A mating type reaction and thus allele specificity is recognised by the ability to dimerise through this domain. Polyclonal antibodies were raised against the b1-1 protein and a heterologous yeast expression system was established for testing potential DNA target sites of the b1-1 and b2-3 proteins, both techniques offering potentially useful tools for further molecular analysis of the A mating type proteins.