Understanding the genetic structure of Gaeumannomyces graminis var. tritici is essential for the establishment of efficient disease control strategies. It is becoming clear that microsatellites， or simple sequence repeats (SSRs)， play an important role in genome organization and phenotypic diversity， and are a large source of genetic markers for population genetics and meiotic maps. In this study， we examined the G. graminis var. tritici genome (1) to analyze its pattern of SSRs， (2) to compare it with other plant pathogenic filamentous fungi， such as Magnaporthe oryzae and M. poae， and (3) to identify new polymorphic SSR markers for genetic diversity. The G. graminis var. tritici genome was rich in SSRs; a total 13，650 SSRs have been identified with mononucleotides being the most common motifs. In coding regions， the densities of tri- and hexanucleotides were significantly higher than in noncoding regions. The di-， tri-， tetra， penta， and hexanucleotide repeats in the G. graminis var. tritici genome were more abundant than the same repeats in M. oryzae and M. poae. From 115 devised primers， 39 SSRs are polymorphic with G. graminis var. tritici isolates， and 8 primers were randomly selected to analyze 116 isolates from China. The number of alleles varied from 2 to 7 and the expected heterozygosity (He) from 0.499 to 0.837. In conclusion， SSRs developed in this study were highly polymorphic， and our analysis indicated that G. graminis var. tritici is a species with high genetic diversity. The results provide a pioneering report for several applications， such as the assessment of population structure and genetic diversity of G. graminis var. tritici.