Genetic diversity is the raw material needed by a species allowing adaptation to changing environmental conditions and thus ensuring long-term sustainability. The development of technologies for environmental genomics provides us with the opportunity to link information, at the whole genome level, with the response of an organism to its natural environment. Over the past 15 years a small tropical fish native to the rivers of India and south Asia, the zebrafish (Danio rerio), has become one of the most popular vertebrate model systems. Zebrafish are abundant and many populations exist that are reproductively isolated. They evolved under distinct environments, and this have lead to genetic diversity and, as a consequence, has created genotypic and phenotypic differences between the populations. For this fish species, a large number of molecular and genomic tools have been developed. As a result, the zebrafish has emerged as a popular model for the study of embryonic development and genetics as well as the study human disease counterparts. The advantages that zebrafish possess, in addition to newly developed large scale screening assays, such as automated in situ hybridization and transgenics for example, has lead to researchers using zebrafish to study toxicogenomics and environmental genomics. Researchers have identified molecular and biochemical pathways, which may not have been observable using standard methods, that are disrupted by some toxin exposures and environmental stressors. These studies will allow us to potentially formulate specific predictions on how vertebrate organisms and populations may be affected by both manmade and natural changes in the environment.