Geohistorical records reveal the long-term impacts of climate change on ecosystem structure. A 5-myr record of mammalian faunas from floodplain ecosystems of South Asia shows substantial change in species richness and ecological structure in relation to vegetation change as documented by stable isotopes of C and O from paleosols. Between 8.5 and 6.0 Ma, C(4) savannah replaced C(3) forest and woodland. Isotopic historical trends for 27 mammalian herbivore species, in combination with ecomorphological data from teeth, show three patterns of response. Most forest frugivores and browsers maintained their dietary habits and disappeared. Other herbivores altered their dietary habits to include increasing amounts of C(4) plants and persisted for >1 myr during the vegetation transition. The few lineages that persisted through the vegetation transition show isotopic enrichment of delta(13)C values over time. These results are evidence for long-term climatic forcing of vegetation structure and mammalian ecological diversity at the subcontinental scale.