Ten microsatellite markers were developed for the fungus Kirramyces gauchensis, which causes an important stem canker disease of Eucalyptus trees in plantations. Primers for 21 microsatellite regions were designed from cloned fragments. Fourteen of the primer pairs provided single amplicons and 10 of these were polymorphic for K. gauchensis. Allelic diversity ranged from 0.21 to 0.76 with a total of 30 alleles. None of the markers was able to amplify in the phylogenetically distinct but morphologically similar species Kirramyces zuluensis. The 10 characterized polymorphic microsatellite regions will be studied to determine the population structure of K. gauchensis in plantations of different countries.