A collection of 168 Cochliobolus miyabeanus isolates was made from cultivated wildrice (Zizania palustris) paddies in Minnesota, USA, during 2007 and 2008. Analysis of 26 polymorphic amplified fragment length polymorphism (AFLP) markers generated with three primer-pair combinations indicated a moderate average gene diversity () of 0·283. Genotypic diversity was high in all collection areas with the exception of a paddy in Itasca County. Significant population subdivision by collection site was found with amova tests using both the entire fungal population data (FST = 0·29, P < 0·001) and the clone-corrected data (FST = 0·08, P < 0·001), and with a Markov chain Monte Carlo approach. Abundant immigrants, shared haplotypes and admixed genotypes were found in paddies in central-eastern areas. Although indirect tests did not support the hypothesis of random mating at the subpopulation level, sexual recombination nevertheless may be possible in areas where both mating type idiomorphs, MAT1-1 and MAT1-2, were found. These results may have implications in breeding for resistance and disease management.