In this study we investigated the relationship between the MAT alpha locus of Cryptococcus neoformans and several MAT alpha-specific mitogen-activated protein (MAP) kinase signal transduction cascade genes, including STE12 alpha, STE11 alpha, and STE20 alpha. To resolve the location of the genes, we screened a cosmid library of the MAT alpha strain B-4500 (JEC21), which was chosen for the C. neoformans genome project. We isolated several overlapping cosmids spanning a region of about 71 kb covering the entire MAT alpha locus. It was found that STE12 alpha, STE11 alpha, and STE20 alpha are imbedded within the locus rather than closely linked to the locus. Furthermore, three copies of MF alpha, the mating type alpha-pheromone gene, a MAT alpha-specific myosin gene, and a pheromone receptor (CPR alpha) were identified within the locus. We created a physical map, based on the restriction enzyme BamHI, and identified both borders of the MAT alpha locus. The MAT alpha locus of C. neoformans is approximately 50 kb in size and is one of the largest mating type loci reported among fungi with a one-locus, two-allele mating system.