Environmental pollutants can have several deleterious properties on living organisms. They can induce acute toxicity, harming cells, tissues, and organs, at high concentrations or high activity. Nonetheless, bioaccumulation resulting from chronic toxification can also be extremely harmful. Plants, as biological indicators, can measure both the actual and potential effects of pollutants when they are used to measure the effects of pollution. Utilizing simple sequence repeats (SSR) and amplified fragment-length polymorphism (AFLP) markers, a "molecular marker fingerprinting" approach was implemented to assess the genotoxic impacts of pollution and determine the environmental risks related to the possible mutagenic effects on three plant species (lettuce, mint, and rocca). DNA from plants exposed to pollution displayed specific marker bands that were not detectable in the DNA of unexposed plants. The development of specific marker band products on the transcription and translation levels will allow for an entirely new understanding of the molecular basis of plants' toxic stress responses to pollution, which appear to reflect the genetic defense action and reaction against pollution. The distinctions between polluted and non-polluted plants seemed to be more pronounced for both markers. Finally, the three plants have a lot of potential to be used as markers of genotoxicity. Genotoxicity in the three plants can be precisely and affordably investigated using SSR and AFLP markers. Conservationists can manage and preserve Egypt's plants, both contaminated and non-polluted, by using the genetics molecular marker bands information from this study.