Both natural environmental processes and anthropogenic activities are responsible for increased rate of contamination in biosphere. Deleterious heavy metals are bioactive and potentially toxic to plants, animals and humans. These pollutants affect organisms on every biological level and leading to toxicity from molecular to ecosystem scale. Heavy metals induced oxidative stress as a result reactive oxygen species (ROS) are generated which are widely implicated in cell membrane and DNA damage.  Arsenic (As) and Lead (Pb) are bioactive toxic metals present in the environment in both organic and inorganic form. Pb and As contamination due to industrial activities such as mining and smelting, energy and fuel production, fertilizers and pesticide application, and exhaust emission from vehicles is increasing day by day.Pb contamination of water and soil is potentially toxic for both plants and human health due to persistence of Pb for long time in air due to soil erosion. Interactions of these metals interrupt several physiological and biochemical processes in plants and could induce genotoxicity events. The plants grown in contaminated soils have elevated level of heavy metals and being non degradable. They enters in food chain via different routes can be passed to various organisms causing many lethal diseases.Developments of PCR based techniques are most important for analysis of the mechanisms of heavy metal tolerance in plants at a biochemical and molecular level. Currently DNA marker techniques are applied to infer all routes through which toxicants may affect the genetic structure of exposed plants/organisms. The random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphism (AFLP) assays are PCR-based techniques and competent of detecting point mutations, temporary alteration of DNA and detection of low doses of pollutants. The changes in RAPD/AFLP profile can be evaluated as alteration in genomic stability test (GTS). The present study is designed to see heavy metal induced changes in Tagetes using RAPD/AFLP assay. Changes in RAPD and AFLP profiles will be compared to biochemical parameters (chlorophyll, carotenoids, proline and Malondialdehyde (MDA) content). Results obtained may suggest that molecular, physiological and biochemical assays could be used together as reliable and powerful biomarkers to determine genotoxic effects of heavy metals in ecotoxicology.