DNA samples from Deschampsia cespitosa and D. flexuosa populations growing in Northern Ontario were analyzed using Inter-simple sequence repeat (ISSR) and microsatellite markers. The mean levels of polymorphic loci detected in populations from the Cobalt, Sudbury, and Manitoulin Islands regions were 46%, 74% and 69%, respectively. ISSR fingerprinting of DNA samples from sites with high metal content revealed low level of polymorphic markers. The between-populations variance contributed only 13.6 % of the total molecular variance while the within-population variance accounts for 71.2%. Using a nonparametric test, we found that between-population differences were significant. The genetic distance data revealed that the D. cespitosa populations from Northern Ontario are different but genetically closely related. No single locus appears to be specific to contaminated sites. A specific ISSR marker differentiating D. cespitosa from D. flexuosa was cloned, sequenced and converted to a SCAR marker. Allelic frequency based on microsatellite analysis of these populations will also be discussed.