Mining and smelting activities from 1800 in the Greater Sudbury Region have caused detrimental effects to the ecosystem. These activities resulted in loss of vegetation leading to liming procedures for revegetation. The objective of the present study was to determine the effect of liming on the ecology and the genetic variation in conifer and hardwood species.  Four pairs of limed and unlimed sites along with three reference sites were analyzed. Shannon diversity index value was significantly higher (1.06) in limed compared to unlimed sites (0.76). Tree species richness values were 4.0, 6.0, 7.7 for unlimed, limed and control sites, respectively. The mean health index revealed significant improvement in population health in limed sites (10.00) compared to unlimed areas (2.50). The highest level of genetic variation was observed in Picea mariana with polymorphisms values ranging from 65% to 90% based on ISSR analyses. The lowest level of polymorphic loci was observed in Pinus resinosa.  For the genetic study various plant species were studied using ISSR marker system. Genetic variations in other conifer and hardwood species analyzed ranged from moderate to high. Overall, all the populations analyzed were genetically sustainable with the exception of Pinus resinosa.