Complex multicellular organisms, such as higher plants and animals, evolved on Earth in an oxygen rich atmosphere 1 . Their tissues, including stem cell niches, require continuous oxygen provision for efficient energy metabolism 2 . Remarkably, maintenance of the pluripotent state of animal stem cells requires hypoxic conditions, whereas higher oxygen tension promotes cell differentiation 3 . Using a combination of genetic reporters and in vivo oxygen measurements, we demonstrate that the plant shoot meristems develop embedded in a low oxygen niche and such hypoxic conditions are required to regulate the production of new leaves. We show that shoot meristem-localised hypoxia inhibits the proteolysis of a novel N-