Plant diversity is important to human welfare worldwide, and this importance is exemplified in subtropical and tropical [(sub)tropical] African savannahs where regional biodiversity enhances the sustaining provision of basic ecosystem services available to millions of residents. Yet, there is a critical lack of knowledge about how savannahs respond to climate change. Here, we report the relationships between savannah vegetation structure, species richness, and bioclimatic variables as recorded by plant biochemical fossils, called biomarkers. Our analyses reveal that the stable carbon isotope composition (δ13C) of discrete sedimentary plant biomarkers reflects vegetation structure, but the isotopic range among plant biomarkers-which we call LEaf Wax Isotopic Spread (LEWIS)-reflects species richness. Analyses of individual biomarker δ13C values and LEWIS for downcore sediments recovered from southeast Africa reveal that the region's species richness mirrored trends in atmospheric carbon dioxide concentration (pCO2) throughout the last 25,000 years. This suggests that increasing pCO2 levels during post-industrialization may prompt future declines in regional biodiversity (1-10 species per unit CO2 p.p.m.v.) through imminent habitat loss or extinction.