Hypoxia is affecting thousands of square kilometers of water and has caused declines in fish populations and major changes in aquatic communities worldwide. For the first time, we report that hypoxia can affect sex differentiation and sex development of zebrafish (Danio rerio), leading to a male-biased population in the F1 generation (74.4% +/- 1.7% males in the hypoxic groups versus 61.9% +/- 1.6% males in the normoxic groups, n = 5; p < 0.05, chi2 test). The increase in males was associated with downregulations of various genes controlling the synthesis of sex hormones (i.e., 3beta-HSD, CYP11A, CYP19A, and CYP19B) as well as an increase in the testosterone/estradiol ratio. The male-dominated populations caused by hypoxia will have reduced reproductive success, thereby threatening the sustainability of natural fish populations.