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Changes in the environment promote variations in fish physiological responses. Genetic variation also plays a role in physiological variation. To explore the role of genetics in physiological variation, we assessed variation of cardiac function (heart rate, stroke volume, and cardiac output), oxygen consumption, yolk conversion efficiency, and cost of development in embryonic and larval AB wild-type and NHGRI-1 zebrafish (low heterozygosity line backcrossed from AB wild-type) exposed to different temperature and oxygen regimes. Fish were exposed from fertilization to 7 days post-fertilization (dpf) to control conditions (28 °C, 21% O2) or to low temperature (23 °C, 21% O2), high temperature (33 °C, 21% O2), moderate hypoxia (28 °C, 13% O2), or severe hypoxia (28 °C, 10% O2). We hypothesized that (1) assessed physiological variables will respond similarly in both fish lines and (2) data variability in the low heterozygosity NHGRI-1 zebrafish will be lower than in AB zebrafish. Cardiac function decreased at lower temperature and in hypoxia in both AB and NHGRI-1 zebrafish. Oxygen consumption was increased by higher temperature and hypoxia in AB fish and by severe hypoxia in NHGRI-1 fish. Yolk conversion efficiency was decreased by lower temperature and hypoxia in AB fish and increased by higher temperature and decreased by hypoxia in NHGRI-1 fish. Cost of development was higher mainly in hypoxia-treated fish. Supporting our hypothesis that genetics contributes to physiological variation, NHGRI-1 zebrafish data showed significantly lower coefficients of variation in 84% of assessed endpoints. We conclude that (1) there is a strong genetic component to physiological variation in fishes and (2) low heterozygosity NHGRI-1 zebrafish are useful models for reducing the ‘noise’ from genetic backgrounds in physiological research in fish, which may aid interpretation of experimental results and facilitate reproducibility.