All sexually fertile strains in the Gibberella fujikuroi species complex are heterothallic, with individual mating types conferred by the broadly conserved ascomycete idiomorphs MAT-1 and MAT-2. We sequenced both alleles from all eight mating populations, developed a multiplex PCR technique to distinguish these idiomorphs, and tested it with representative strains from all eight biological species and 22 additional species or phylogenetic lineages from this species complex. In most cases, either an ϳ800-bp fragment from MAT-2 or an ϳ200-bp fragment from MAT-1 is amplified. The amplified fragments cosegregate with mating type, as defined by sexual cross-fertility, in a cross of Fusarium moniliforme (Fusarium verticillioides). Neither of the primer pairs amplify fragments from Fusarium species such as Fusarium graminearum, Fusarium pseudograminearum, and Fusarium culmorum, which have, or are expected to have, Gibberella sexual stages but are thought to be relatively distant from the species in the G. fujikuroi species complex. Our results suggest that MAT allele sequences are useful indicators of phylogenetic relatedness in these and other Fusarium species.Fusarium isolates in the Gibberella fujikuroi species complex include important fungal pathogens of agricultural crops and trees and may be divided into at least eight different biological species and 32 additional asexual species or phylogenetic lineages (4, 10, 13, 15, 16). All sexually fertile species in the G. fujikuroi species complex are dimictic, i.e., two isolates are cross-fertile if they carry the different mating-type idiomorphs MAT-1 and MAT-2 (4, 6, 9, 13), which share no sequence similarity with respect to either DNA sequence or the proteins encoded (5). The MAT-2 idiomorphs thus far characterized have a conserved HMG (high-mobility-group) domain (3,5,6,9). The MAT-1 idiomorphs have a conserved ␣-domain (5, 25), but no MAT-1 alleles have yet been described from any members of the G. fujikuroi species complex.Our objectives in this study were (i) to sequence conserved portions of the MAT-1 and MAT-2 alleles from the eight known G. fujikuroi mating populations, (ii) to develop a multiplex PCR reaction to be used for the identification of both mating-type idiomorphs within the defined biological species of the G. fujikuroi species complex, (iii) to determine the range of Fusarium species which have Gibberella teleomorphs to which this technique can be successfully applied, and (iv) to test the use of the sequence of the MAT idiomorphs for phylogenetic analyses. This technique eases the identification of strains to be used in crosses to identify new biological species and eliminates the need for sexual crosses to score this trait. MAT sequence variations may be used as phylogenetic characters, providing another marker that can be used to test phylogenies for robustness.