Riding the wave of advances in material sciences in the 21st century, a significant number of new and innovative chemicals have been introduced into various sectors of human society. At the same time, concerns have been raised about the environmental implications of many new chemicals for the health of humans and the environment. Addressing these concerns requires the application of most up-to-date technologies. Over the past six years, a tremendous revolution has occurred in sequencing technologies, which has already had a profound impact on our understanding of chemical screening, risk assessment, and predictive toxicology. However, the NGS technique used in environmental toxicology is still in its infancy, such as screening of genetic biomarkers related to various adverse outcomes due to chemical exposures. Hence, these researchers are investigating the applications of toxicogenomics using NGS for emerging contaminants of concern in aquatic environments such as the Great Lakes.