Randomly amplified polymorphic DNA (RAPD) markers and mating type were used to examine regional population structure of Setosphaeria turcica in the eastern United States. Of 251 maize-infecting isolates studied, 155 multilocus haplotypes were identified using 21 RAPD markers. Twelve isolates of the most common haplotype were identified from seven states and represented 5.2% of the sample. Although variation in genetic diversity was greatest within states rather than between either regions or states within regions, multidimensional scaling based on average taxonomic distances among state samples showed a close association of samples from IL, OH, IN, IA, MN, MI/WI, and NC. Isolates from GA/SC, VA/TN, PA/NY, and FL were distant from this core group that included midwestern states and NC and were distinct from one another. The high genotypic diversity, near equal mating type frequencies, and gametic phase equilibrium in samples from several states are inconsistent with a strictly clonal population. The population genetic structure of S. turcica is likely the result of both asexual and sexual reproduction. It is not clear whether sexual recombination actually occurs in the eastern United States or occurs elsewhere in tropical America and recombinant genotypes migrate to North America.