Many aerobic organisms have developed molecular mechanism to tolerate hypoxia, but the specifics of these mechanisms remain poorly understood. It is important to develop genetic methods that confer increased hypoxia tolerance to intensively farmed aquatic species, as these are maintained in environments with limited available oxygen. As an asparaginyl hydroxylase of hypoxia-inducible factors (HIFs), factor inhibiting HIF (FIH) inhibits transcriptional activation of hypoxia-inducible genes by blocking the association of HIFs with the transcriptional coactivators CREB-binding protein (CBP) and p300. Therefore, here we sought to test whether is involved in regulating hypoxia tolerance in the commonly used zebrafish model. Overexpressing the zebrafish gene in epithelioma papulosum cyprini (EPC) cells and embryos, we found that inhibits the transcriptional activation of zebrafish HIF-α proteins. Using CRISPR/Cas9 to obtain-null zebrafish mutants, we noted that the deletion makes zebrafish more tolerant of hypoxic conditions than their WT siblings, but does not result in oxygen consumption rates that significantly differ from those of WT fish. Of note, we identified fewer apoptotic cells in adult-null zebrafish brains and in -null embryos, possibly explaining why the-null mutant had greater hypoxia tolerance than the WT. Moreover, the deletion up-regulated several hypoxia-inducible genes in-null zebrafish exposed to hypoxia. The findings of our study suggest that plays a role in hypoxia tolerance by affecting the rate of cellular apoptosis in zebrafish.