The mammalian circadian system consists of a master clock in the brain that synchronizes subsidiary oscillators in peripheral tissues. The master clock maintains phase coherence in peripheral cells through systemic cues such as feeding-fasting and temperature cycles. Here, we examined the role of oxygen as a resetting cue for circadian clocks. We continuously measured oxygen levels in living animals and detected daily rhythms in tissue oxygenation. Oxygen cycles, within the physiological range, were sufficient to synchronize cellular clocks in a HIF1α-dependent manner. Furthermore, several clock genes responded to changes in oxygen levels through HIF1α. Finally, we found that a moderate reduction in oxygen levels for a short period accelerates the adaptation of wild-type but not of HIF1α-deficient mice to the new time in a jet lag protocol. We conclude that oxygen, via HIF1α activation, is a resetting cue for circadian clocks and propose oxygen modulation as therapy for jet lag. Display omitted •O2 levels exhibit daily rhythms in blood and tissue of rodents•Physiological O2 rhythms reset clocks in cultured cells in HIF1α-dependent manner•Several core clock genes respond to changes in O2 levels in HIF1α-dependent fashion•Modulation of O2 levels accelerates the recovery of mice in a jet lag protocol Adamovich et al. uncover daily oscillations in blood and tissue oxygenation and find that physiological oxygen rhythms synchronize clocks in cultured cells in a HIF1α-dependent manner. Modulation of oxygen levels accelerates the recovery of wild-type but not of HIF1α-deficient mice to the new time in a jet lag protocol.