In the bipolar basidiomycete, Pholiota nameko, the homeodomain protein, A4-hox1, located at the A mating-type locus, is known to regulate mating compatibility. In the present study, we investigated the genomic structure of the P. nameko A mating-type locus and its flanking region. A second homeodomain gene (A4-hox2) was discovered upstream of A4-hox1; this together with the conserved gene order around the A mating-type locus and their similar transcription direction were found in P. nameko, another bipolar mushroom, Coprinellus disseminatus, and two tetrapolar mushrooms, Coprinopsis cinerea and Laccaria bicolor. Analysis of the deduced protein sequences of the homeodomain protein genes from two strains of P. nameko show that the putative functional domains differ from those of the homeodomain proteins of the tetrapolar mushrooms, C. cinerea and L. bicolor. Crown Copyright (C) 2008 Published by Elsevier Ltd on behalf of The British Mycological Society. All rights reserved.