The aim of our research was the selection of sensitive plant and animal test-objects and biomarkers for assessment of genotoxic effects of water and soil pollution in Armenia. Water genotoxicity was evaluated in four sites of Lake Sevan basin. The levels of DNA damage in erythrocytes of fish C. auratus gibelio and hemocytes of crayfish A. leptodactylus from more polluted estuaries of Gavaraget and Dzknaget Rivers and micronuclei (MN) frequency in tradescantia (clone 02), treated with corresponding water samples, were significantly higher compared to results, obtained from less polluted areas near village Shorzha and Peninsula of Lake Sevan. The significant positive correlation between DNA and chromosome damage and content of NO3, Si, Mn and Cu in water was revealed for all applied bioindicators. Levels of DNA damage in erythrocytes of bisexual lizards D. raddei from the more polluted Kajaran town were significantly higher compared with lizards from the less polluted villages Zuar, Lchap and nature reserve “Shikahogh”. The level of DNA damage in parthenogenetic lizard D. armeniaca caught in more polluted Vanadzor town was significantly higher compared with lizards from less polluted village Privolnoe. The significant positive correlation was revealed between DNA damage and MN frequency in lizards D. raddei and content of As, Cu, V and Mo in soil, and between DNA damage in lizards D. armeniaca and content of Cu and Mo in soil. Higher level of soil genotoxicity in Kapan town compared with nature reserve “Shikahogh” demonstrated using MN assay in tradescantia. The significant correlation between MN frequency in tradescantia and content of As, Cu, Zn, V, Mo, Pb and Cd in soils was revealed. The results obtained suggest that genetic damage in organisms living in polluted water and soil ecosystems are impacted by the presence of heavy metals.