Solar luminosity on the early Earth was significantly lower than today. Therefore, solar luminosity models suggest that, in the atmosphere of the early Earth, the concentration of greenhouse gases such as carbon dioxide and methane must have been much higher(1,2). However, empirical estimates of Proterozoic levels of atmospheric carbon dioxide concentrations have not hitherto been available. Here we present ion microprobe analyses of the carbon isotopes in individual organic-walled microfossils extracted from a Proterozoic (similar to1.4-gigayear-old) shale in North China. Calculated magnitudes of the carbon isotope fractionation in these large, morphologically complex microfossils suggest elevated levels of carbon dioxide in the ancient atmosphere-between 10 and 200 times the present atmospheric level. Our results indicate that carbon dioxide was an important greenhouse gas during periods of lower solar luminosity, probably dominating over methane after the atmosphere and hydrosphere became pervasively oxygenated between 2 and 2.2 gigayears ago.