Technical Abstract: Fusarium isolates associated with the Gibberella fujikuroi species complex include many important fungal pathogens of agricultural crops and trees. In this study an interspecific hybrid between F. circinatum and F subglutinans was used to compile a genetic linkage map. A framework map was constructed using a total of 578 AFLP markers together with the mating type (MAT-1 and MAT-2) genes and the histone (H3) gene. Twelve major linkage groups were identified (n=12) in Fusarium. Fifty percent of the markers showed significant deviation from the expect 1:1 transmission ratio in a haploid F1 cross (P<0.05). The transmission of the markers on the linkage map was biased towards alleles of the F. subglutinans parent, with an estimated 60% of the genome of F1 individuals contributed by this parent. This map will serve as a powerful tool to study the genetic architecture of interspecific differentiation and pathogenicity in the two parent genomes.