Microorganisms play an important role in cycling of elements of ecosystems, including a wide range of chemical pollutants from anthropogenic origin. These pollutants in ecosystems, particularly aquatic, and sediment and soils, are in different physical and chemical forms in association with the inorganic and organic constituents of the sediment and soils, resulting in variable availability of them to microorganisms for assimilation and transformation. A thorough and comprehensive knowledge of the physical and chemical states of them in the environments requires detailed information of both the bioavailable pollutant concentration and also the metabolic capability of the microorganisms to assess the ecological and environmental toxicity of these pollutants meaningfully. Apart from the primary role as decomposers, microorganisms are qualified to be sensitive indicators for environmental pollution, and ecological health and ecotoxicity of pollutants because of their very short generation time and quickly response to chemical pollutants than higher and large organisms. When used for testing with the same strain, different laboratories can generate high reproducible results to allow comparison of the data feasible, not mention the reduction in cost. Based on the current advances made on genomics analysis and bioinformatics, microbial genomes are easily assembled with the technologies available to providing useful transcriptomic and metabolic annotations, expression and prediction to allow advance toxicological to another level.