Fine metabolic regulation to adjust for changes in oxygen and energy availability is a conserved, ubiquitous survival strategy of cells and tissues to unpredictable environments. Severe oxygen deprivation can overwhelm these protective strategies and is a common cause of major brain, heart, and kidney injury in adults and newborns alike. Intriguingly, mild hypoxia can be preventative against a later, more severe hypoxia exposure via “hypoxic preconditioning”—a protective phenomenon that is not yet fully understood. We have therefore established and optimized an embryonic zebrafish model to study hypoxic preconditioning in detail using a functional genomic approach. Using this developmental zebrafish model, we validated five novel hypoxia-protective genes from hundreds of hypoxia-regulated genes we identified via differential expression microarray: irs2a, crtc3, and camk2g2 have been previously implicated in insulin and glucose metabolism, while btr01 and ncam2 are previously uncharacterized. Furthermore, we have generated null mutants using CRISPR in three of these genes (irs2a, crtc3, btr01) and have begun to characterize hypoxia-induced cellular and transcriptional mutant phenotypes. These results extend our understanding of the mechanisms of hypoxic preconditioning and affirm the discovery potential of this novel vertebrate hypoxic stress model.