Carbon-isotope values of bulk organic matter from high-altitude lakes on Mount Kenya and Mount Elgon, East Africa, were 10 to 14 per mil higher during glacial times than they are today. Compound-specific isotope analyses of leaf waxes and algal biomarkers show that organisms possessing CO2-concentrating mechanisms, including C-4 grasses and freshwater algae, were primarily responsible for this large increase. Carbon limitation due to lower ambient CO2 partial pressures had a significant impact on the distribution of forest on the tropical mountains, in addition to climate. Hence, tree line elevation should not be used to infer palaeotemperatures.