The last 10 years have seen the introduction and widespread adoption of toxicogenomic techniques in the aquatic toxicology research community 1-3. While initial research efforts primarily examined gene expression using gene macro- and microarrays, recent efforts now include other “Omics” approaches, and exciting discoveries have been made using both proteomics and metabolomics. In recent years, Omics-based technologies – those disciplines focused on the large-scale study of genomes, proteomes, and metabolomes – have had an impressive impact in diverse fields, and have been responsible for a number of novel research discoveries in aquatic toxicology. International recognition of the power of these molecular approaches has prompted discussions about the incorporation of Omics-based endpoints in environmental monitoring programs and ecological modeling to predict population level effects 4. Recent developments in ultra high-throughput sequencing, often referred to as next-generation sequencing technologies, represent a powerful tool for discovery in eotoxicogenomics applications. Perhaps most promising are the opportunities for molecular applications in non-model species. Next-generation sequencing offers exciting opportunities for using molecular techniques beyond a handful of traditional model species by allowing the production of high-quality genomic and transcriptomic libraries for species of toxicological and ecological significance. In addition, the areas of environmental biomonitoring and barcoding, genetic variation and adaptation to pollutants, and ecotoxico-genomics and proteomics to decipher chemical mode of action have benefited tremendously from these technologies. With initial barriers associated with the adoption of these techniques rapidly decreasing, Omics technologies are poised to become a feasible option for a wider range of species-specific applications. The SETAC North America 30th Annual Meeting showcased a session devoted specifically to Omics applications in aquatic toxicology. The purpose of the symposium was to highlight the newest advances in genetics and ecotoxicogenomics, proteomics, and metabolomics as applied towards aquatic toxicology and ecology. Several of the speakers demonstrated the extent and sophistication of the methods to explore questions of importance to ecotoxicology and ecology. One area addressed by several investigators was the advances in metagenomics. The introduction of next generation sequencing has made it possible to sequence bulk environmental samples from complex biological sources, such as macrobenthic invertebrates that inhabit estuarine sediments, groundwaters, and soil environments. This technology is able to quickly assess the diversity of multiple phyla from an ecologically relevant sampling scheme. This approach can be rapid and cost-effective and offers more accurate information on the relative abundance of taxa and how the community structure is affected by changing environmental conditions. Presentations also addressed pyrosequencing for environmental barcoding to assess biodiversity in ecosystems for the Barcode of Life Data Systems (BOLD). Currently, information has been gathered for more than 50,000 species of eukaryotes, including many aquatic species. However, the work has been very challenging because multiple life stages are often present (larvae and adults). A primary goal of high-throughput sequencing in metagenomics is to amass large datasets for incorporation into ecological risk assessments in the future. While significant achievements have been made in bioinformatics for this approach, challenges still lie ahead for the storage of large datasets. Pyrosequencing approaches also have been used to assess differences between genetic diversity among fish populations inhabiting polluted and clean environments by identifying single nucleotide polymorphisms. Genetic markers of a reference and a polluted site can be compared to determine if genetic signatures exist for adaptive responses in contaminated habitats. Gene expression signatures also can be compared to genetic diversity to locate expression quantitative trait loci, regions of chromosomes that are correlated to a phenotypic response—in this case, gene expression. This approach can be labor intensive and requires expertise in both genomics and quantitative genetics, but it is beneficial for the community as a whole to dissect the genetic basis for coping with chemical stressors. There is a current knowledge gap in aquatic toxicology on population divergence and adaptation that may be driven by aquatic pollutants. To complement ecotoxicogenomics, ecotoxicoproteomics is in its infancy and promises to be a significant biomarker discovery method in aquatic toxicology. For example, the use of 2D gel electrophoresis followed by time of flight mass spectrometry has been a powerful approach for protein biomarker discovery in aquatic species and is reviewed in this issue. In addition to gel-based methods, non-gel based proteomics, such as redox and quantitative proteomics, will also contribute to a growing toolbox in ecotoxicology and environmental science. If genes and proteins are to be incorporated into predictive models on a larger scale, a better understanding of how these two entities relate on a temporal scale is required 5. Efforts to address these relationships in fish using Omics technologies have been made 6, 7. One approach that has yet to be explored for aquatic toxicology is the use of post-translational protein modifications as biomarkers of chemical exposure. Metabolomics describes the quantitative measurement of the dynamic metabolic response of a living system to a toxic or physiological challenge and, as such, is arguably more relevant physiologically than genes or proteins. With this method, it is possible to analyze metabolites in a variety of tissues, including urine, to obtain unique metabolite profiles that are chemical-specific. The advantage of urine is that multiple samples can be collected from the same individual to study compensatory responses and recovery from exposure. The Omics symposium also highlighted the movement towards metabolic profiling in cell cultures to reduce animal models. The role of metabolomics for studying physiological responses in aquatic organisms will undoubtedly continue to expand. A paradigm shift in the use of molecular endpoints has occurred over the last 10 years, from studies focused on single products to those studying multiple products at once to assess global patterns of response. This symposium demonstrated the application of new methods in Omics technologies for increasing understanding of how environmental stressors may have pleiotropic effects in vivo and perturb multiple cell pathways. As pointed out by a recent international consortium on toxicogenomics 4, we need better understanding of the relationships between specific molecular biomarkers and ecological adverse events and a better understanding of how molecular markers relate to one another (i.e., DNA variation-gene expression-protein-metabolism) to produce a phenotype. To assist with the rapidly growing datasets, new bioinformatics approaches are required to assimilate and integrate data. This will be a significant advance for aquatic toxicology and biomarker discovery. It will become less important to identify individual genes, proteins, and metabolites as biomarkers and more important to identify cell pathways affected by a chemical stressor. Emerging methods at the transcriptional level target changes in transcriptional factors and their use to reverse engineer regulatory networks that may be impacted by a pollutant. Gene set enrichment analysis is also underutilized in aquatic toxicology to discover novel pathways altered by endocrine disrupting chemicals. This approach utilizes significantly more information than functional enrichment methods, using all genes involved in a pathway to determine whether or not a given pathway is altered in its entirety. Undoubtedly, mapping the interactome and gene regulatory networks using reverse engineering will be a powerful approach in aquatic toxicology. Cost, training, bioinformatics capabilities, and complexity of individual responses remain obstacles, but improved gene annotation of non-model species, dissection of genotype-phenotype temporal relationships, and identification of molecular interactions (systems ecology and ecotoxicology) can help overcome these roadblocks. Tremendous advances have been made toward circumventing these limitations in only a few years. As DNA sequencing technology becomes more widespread and computer algorithms improve, it will be exciting to follow the impact Omics technologies will have in aquatic ecology and toxicology in the upcoming decade.