Abstract: A parent cross between two deoxynivalenol-producing Gibberella zeae FG24 (Szeged, Hungary) x FG3211 (Sersheim, Germany) belonging to lineage 7 was analysed for segregation of polymorphic markers among 153 progeny using Amplified Fragment Length Polymorphism (AFLP) and Random Amplified Polymorphic DNA (RAPD). Fifty six RAPD primers and 31 AFLP primer combinations were screened for polymorphism between the parents. High proportion of segregation distortion among progeny was observed using selected primers. Genetic distance of the two parents was compared to isolates lineage 7, Z-3639 (Kansas) and lineage 6, R-5470 (Japan). Rate of polymorphism between Z-3639 and R-5470 was about three to four times greater than between FG24 and FG3211. Isolate Z-3639 was closely associated to FG24 and FG3211 whereas R-5470 was genetically separated based on cluster analysis, thus confirming their lineage grouping. Genetic distances among the four parents using AFLP and RAPD markers were correlated, but association between molecular markers and the aggressiveness of G. zeae population could not be established. The high level of genetic similarity of the two European parents does not support the high genetic diversity of lineage 7 to which these two isolates belonged. Polymorphism of lineage 7 parent isolates to be used is one of important considerations in genetic mapping of G. zeae.