Microsatellite markers of Crinipellis perniciosa, with three and four repeats, were developed from sequence database and evaluated for their usefulness in detecting genetic polymorphism. Thirty-three primers produced unambiguous amplification products of 28 microsatellite-containing loci and 14 microsatellite-like polymorphic loci, with two to seven alleles at each locus. Three loci were useful to distinguish isolates from different biotypes and isolates from different countries. Amplification of the markers in the closely related fungi Moniliophthora roreri indicates that their usefulness in population's studies may go beyond the present study of the C. perniciosa and may have applications in population genetics of M. roreri.