All embryonic and fetal amniotes possess a ductus(i) arteriosus(i) that allows blood to bypass the pulmonary circulation and the non-functional lungs. The central hemodynamic of embryonic reptiles are unique, given the additional systemic aorta that allows pulmonary circulatory bypass, the left aorta (LAo). The LAo exits in the right ventricle or ‘pulmonary side’ of reptilian hearts in both embryos and adults, but its functional significance in ovo is unknown. This study investigated the role of the LAo in embryonic American alligators by surgically occluding the LAo and measuring oxygen consumption and, in addition, measured hemodynamic responses to hypoxia in embryonic alligators. We measured systemic cardiac output and primary chorioallantoic membrane (CAM) artery blood flow for normoxic and hypoxic-incubated (10% O2) American alligator embryos (Alligator mississippiensis). Chronic blood flow (1–124 h) in the primary CAM artery for hypoxic-incubated embryos (92 ± 26 ml min−1 kg−1) was elevated when compared with normoxic-incubated embryos (29 ± 14 ml min−1 kg−1, N = 6; P = 0.039). For hypoxic-incubated embryos, acute LAo blood flow (49.6 ± 24.4 ml min−1 kg−1) was equivalent to the combined flow of the three systemic great vessels that arise from the left ventricle, the right aorta, common carotid and subclavian arteries (43.6 ± 21.5 ml min−1 kg−1, N = 5). Similarly, for normoxic-incubated embryos, LAo blood flow (27.3 ± 6.6 ml min−1 kg−1) did not statistically differ from the other three vessels (18.4 ± 4.9 ml min−1 kg−1, N = 5). This study contains the first direct test of LAo function and the first measurements of blood flow in an embryonic reptile. These data support the hypotheses that embryonic alligators utilize the LAo to divert a significant amount of right ventricular blood into the systemic circulation, and that CAM blood flow increases following chronic hypoxic conditions. However, surgical occlusion of the LAo did not affect egg supporting the hypothesis that the LAo of reptiles is not critical to maintain in ovo oxygen consumption.Electronic supplementary materialThe online version of this article (doi:10.1007/s00360-010-0494-6) contains supplementary material, which is available to authorized users.