The volatile organic compound isoprene is produced by many plant species, and provides protection against biotic and abiotic stresses1. Globally, isoprene emissions from plants are estimated to far exceed anthropogenic emissions of volatile organic compounds2. Once in the atmosphere, isoprene reacts rapidly with hydroxyl radicals3 to form peroxy radicals, which can react with nitrogen oxides to form ground-level ozone4. Here, we use canopy-scale measurements of isoprene fluxes from two tropical ecosystems in Malaysia-a rainforest and an oil palm plantation-and three models of atmospheric chemistry to explore the effects of isoprene fluxes on ground-level ozone. We show that isoprene emissions in these ecosystems are under circadian control on the canopy scale, particularly in the oil palm plantation. As a result, these ecosystems emit less isoprene than present emissions models predict. Using local-, regional- and global-scale models of atmospheric chemistry and transport, we show that accounting for circadian control of isoprene emissions brings model predictions of ground-level ozone into better agreement with measurements, especially in isoprene-sensitive regions of the world. © 2011 Macmillan Publishers Limited. All rights reserved.