Genetic differences between 20 Chinese wheat (Triticum aestivum L.) landraces highly resistant to Fusarium head blight (FHB) and 4 wheat lines highly susceptible to FHB were evaluated by means of microsatellite markers, in order to select suitable parents for gene mapping studies. Thirty-nine out of 40 microsatellite markers (97.5%) were polymorphic among the 24 wheat genotypes. A total of 276 alleles were detected at the 40 microsatellite loci. The number of alleles per locus ranged from 1 to 16, with an average of 6.9 alleles. Among these microsatellite loci, the largest polymorphism information content (PIC) value was 0.914 (GWM484), while the lowest PIC value was 0 (GWM24). The mean genetic similarity index among the 24 genotypes was 0.419, ranging from 0.103 to 0.673. Clustering analysis indicated that the highly susceptible synthetic wheat line RSP was less genetically related to and more divergent from the Chinese highly resistant landraces. These results were useful in the identification of suitable parents for the development of mapping populations for tagging the FHB resistance genes among these Chinese wheat landraces.