In the current studies, we sequenced and characterized the gene for the homeodomain protein (hox1) in a bipolar mushroom, Pholiota nameko, which is a putative homologue of A mating type genes in the tetrapolar basidiomycete, Coprinopsis cinerea. We also sequenced and characterized the gene for the pheromone receptor (rcb1) in P. nameko, which is a putative homologue of the B mating type genes in C. cinerea. Restriction fragment length polymorphism (RFLP) and linkage analyses indicated that the both genes are present as a single locus on the different chromosome. Moreover, in P. nameko, the hox1 gene was mapped to the A mating type locus in linkage group I. However, rcb1 was not linked to the A mating type locus and was mapped to the other linkage group. These results strongly suggest that hox1 regulates with incompatibility in the bipolar mushroom, and that rcb1 may not affect the mating function in P. nameko. This is the first report regarding the structure of the mating type genes in bipolar mushrooms.