The aim of this study was to give a comparative overview of diversity in Gaeumannomyces graminis var. tritici (Ggt), the take-all plant pathogenic fungus. For this, 98 Ggt isolates of a worldwide collection were first compared with two sets of specific PCR tools that discriminate G1/G2 and A/B genetic groups. A correspondence was found between G1 and B on the one hand and between G2 and A on the other, and less frequent divergent genotypes were also found. For more insight into Ggt diversity, a deeper phylogenetic analysis was conducted with the DNA sequences of two regions: the coding region of the RAPD-PCR marker previously selected and used for genotyping G1/G2 isolates, corresponding to the gentisate 1,2-dioxygenase-like gene, and the rDNA region corresponding to a part of the 18S gene, 5.8S gene, ITS1 and ITS2 DNA sequences. The distribution of Ggt genotypes into two main groups was confirmed by this phylogenetic analysis. The results give some evidence of the congruence of the molecular markers used by different teams and describe for the first time at the level of a worldwide collection two major genetically different groups of Ggt. The use of a universal molecular descriptor of Ggt groups is useful for investigating the occurrence, distribution and changes in Ggt populations in relation to epidemic dynamics.