Stable light isotopes in ratite eggshells have been shown to be reliable indicators of shifts in climate and environmental conditions in the past. Here, we show that δ 18 O and δ 13 C values in fossil and modern ratite eggshells collected in the aeolianite deposits of the southern and central Namib Desert track regional distinctions and global climate shifts throughout the Neogene. δ 18 O values, although variable, are consistently higher in the central compared to the southern Namib throughout the record. δ 18 O trends during the Miocene differ for the two regions, but track each other post-Miocene. Throughout the Miocene, δ 13 C values for ratite eggshells from both the central and southern Namib regions are indistinguishable showing that the flora remained C 3 throughout. The overall negative (−3‰) shift in mean values for Miocene biostratigraphic zones is consistent with the response of C 3 photosynthesis to pCO 2 shifts from 180 to 320ppmv as estimated from marine alkenone studies and/or evolution of the δ 13 C of the atmospheric CO 2 . Evidence for C 4 plants occurs post-Miocene, with the development of the southern, winter rainfall and central/northern, summer rainfall zonation apparent today. These data provide independent corroboration that the expansion of C 4 -dominated ecosystems after ∼ 7 Ma cannot be attributed to a reduction of pCO 2 below a 500 ppmv threshold, as earlier proposed. Proliferation of C 4 plants in the Namib after ∼5 Ma and, elsewhere, may be related rather to energy budgets and rainfall seasonality shifts resulting from large-scale atmospheric and oceanic circulation reorganisation.