An adequate supply of oxygen is important for the survival of all tissues, but is especially critical for tissues with high energy demands such as the heart. Insufficient tissue oxygenation occurs under a variety of conditions, including high altitude, embryonic and fetal development, inflammation, and thrombotic diseases, often affecting multiple organ systems. Responses and adaptations of the heart to hypoxia are of particular relevance in human cardiovascular and pulmonary diseases, where the effects of hypoxic exposure can range in severity from transient to long-lasting. This study uses the genetic model system Drosophila to investigate cardiac responses to acute (30 minutes), sustained (18 hours), and chronic (3 weeks) hypoxia with reoxygenation. Whereas hearts from wild type flies recovered quickly after acute hypoxia, exposure to sustained or chronic hypoxia significantly compromised heart function upon reoxygenation. Hearts from flies with mutations in sima, Drosophila homolog of the Hypoxia Inducible Factor alpha subunit (HIFα), exhibited exaggerated reductions in cardiac output in response to hypoxia. Heart function in hypoxia-selected flies, selected over many generations for survival in a low oxygen environment, revealed reduced cardiac output in terms of decreased heart rate and fractional shortening compared to their normoxia controls. Hypoxia-selected flies also had smaller hearts, myofibrillar disorganization and increased extracellular collagen deposition, consistent with the observed reductions in contractility. This study indicates that longer duration hypoxic insults exert deleterious effects on heart function that are mediated in part by sima and advances Drosophila models for the genetic analysis of cardiac-specific responses to hypoxia and reoxygenation.