The white-rot basidiomycete fungus Phanerochaete chrysosporium (Agaricomycetes) is a model species that produces potent wood-degrading enzymes. The mating system of the species has been difficult to characterize due to its cryptic fruiting habit and lack of clamp connections in the heterokaryotic phase. By exploiting the draft genome sequence, we reevaluated the mating system of P. chrysosporium by studying the inheritance and segregation of putative mating-type gene homologues, the homeodomain transcription factor genes (MAT-A) and the pheromone receptors (MAT-B). A pattern of mating incompatibility and fructification consistent with a bipolar system with a single MAT locus was observed, but the rejection response was much weaker than that seen in other agaricomycete species, leading to stable heterokaryons with identical MAT alleles. The homeodomain genes appear to comprise the single MAT locus because they are heterozygous in wild strains and hyperpolymorphic at the DNA sequence level and promote aspects of sexual reproduction, such as nuclear migration, heterokaryon stability, and basidiospore formation. The pheromone receptor loci that might constitute a MAT-B locus, as in many other Agaricomycetes, are not linked to the MAT-A locus and display low levels of polymorphism. This observation is inconsistent with a bipolar mating system that includes pheromones and pheromone receptors as mating-type determinants. The partial uncoupling of nuclear migration and mating incompatibility in this species may be predicted to lead to parasexual recombination and may have contributed to the homothallic behavior observed in previous studies.The mushroom-forming fungi, Agaricomycetes (Basidiomycota), have a mating system in which compatible haploid mycelia (homokaryons) exchange nuclei to form mated mycelia (heterokaryons) that are comprised of cells with two compatible nuclear types (mating types). Once mated, heterokaryons function as genetic diploids, but the two nuclear types divide together in an unfused state until karyogamy occurs in the basidial cells of the fruiting body immediately prior to meiosis and spore formation. In the model mushroom species (e.g., Coprinopsis cinerea and Schizophyllum commune), heterokaryons are termed dikaryons because each cell contains exactly two nuclei, but in a large number of Agaricomycetes species (e.g., 20 to 30% of the nongilled forms [10]), the hyphal cells of heterokaryons are multinucleate. In these fungi (variously termed multinucleate, plurinucleate, or holocenocytic), each cell presumably contains both mating types but a variable number of nuclei per cell, for example, up to 12 nuclei per cell were observed in the termite symbiont Termitomyces (15) and as many as 69 per cell in Wolfiporia extensa (34).In dikaryotic fungi, differentiating homokaryotic from heterokaryotic phases is readily accomplished by observing the characteristic clamp connections or hook cells that function in the maintenance of the binucleate state (43). In contrast, species with multinucleate heterok...