Several decades of sulfuric acid and other mineral emissions from smelters has had a huge impact on Northern Ontario ecosystems. The main objective of this study is to compare the levels of genetic variation among and within red maple populations from areas with different metal contents within the Greater Sudbury Region. Soil from contaminated and uncontaminated sites was analyzed to determine the current levels of metal content in the ecosystems. There were higher levels of metals in soil samples from sites from Sudbury within 15km from the smelters compared to the control sites. No significant differences in pH were found among the sites since all the values were typical of the Canadian Shield ranges. Physiological analysis suggests that red maple trees accumulate metals in branches and leaves. ISSR analysis revealed the level of polymorphic loci ranging from 58% to 75%. The level of genetic variation was higher in control sites than in metal contaminated sites. The populations analyzed were genetically closely related but two different groups were identified. The results of the present study indicate that red maple populations in the Greater Sudbury Region in Northern Ontario are sustainable despite high levels of heavy metals in soils.