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 δ18O and δ13C 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. δ18O values, although variable, are consistently higher in the central compared to the southern Namib throughout the record. δ18O trends during the Miocene differ for the two regions, but track each other post-Miocene. Throughout the Miocene, δ13C values for ratite eggshells from both the central and southern Namib regions are indistinguishable showing that the flora remained C3 throughout. Keywords: Miocene, ratite eggshells, Namib Desert, stable isotopes, pCO2, C4 expansion.