The oxygenation of the deep ocean in the geological past has been associated with a rise in the partial pressure of atmospheric molecular oxygen (O 2 ) to near-present levels and the emergence of modern marine biogeochemical cycles1,2,3,4,5. It has also been linked to the origination and diversification of early animals3,5,6,7. It is generally thought that the deep ocean was largely anoxic from about 2,500 to 800 million years ago1,2,3,4,5,6,7,8,9,10,11,12, with estimates of the occurrence of deep-ocean oxygenation and the linked increase in the partial pressure of atmospheric oxygen to levels sufficient for this oxygenation ranging from about 800 to 400 million years ago3,5,7,11,13. Deep-ocean dissolved oxygen concentrations over this interval are typically estimated using geochemical signatures preserved in ancient continental shelf or slope sediments, which only indirectly reflect the geochemical state of the deep ocean. Here we present a record that more directly reflects deep-ocean oxygen concentrations, based on the ratio of Fe3+ to total Fe in hydrothermally altered basalts formed in ocean basins. Our data allow for quantitative estimates of deep-ocean dissolved oxygen concentrations from 3.5 billion years ago to 14 million years ago and suggest that deep-ocean oxygenation occurred in the Phanerozoic (541 million years ago to the present) and potentially not until the late Palaeozoic (less than 420 million years ago).