The 13C/12C isotope ratios in animal1 and human2 bone can be used as indicators of diet, more recently it was shown that the 15N/14N ratios of animals and humans are similarly determined by the food they eat3–5. Specifically, the stable carbon isotope composition reflects the proportion of C3 and C4 plants at the base of the food chain1,2, while both 15N and 13C reveal the difference between a marine and terrestrial diet in modern as well as archaeological contexts5–7. Here we present data for human and animal bones from southern Africa which only partly conform to previously recognized patterns for 15N/14N ratios. Prehistoric human bones from a particular coastal region of South Africa show 15N/14N ratios consistent with the marine and terrestrial diets indicated by the 13C/12C ratios, but bones of both prehistoric humans and modern wild animals from a larger part of the subcontinent show variations in 15N/14N ratios which cannot be ascribed to known variations in diet. It appears that, in some environments, nitrogen isotope studies must also take into account the possible influence of the climate.