One of the most promising new tools for examining diet and habitat niche in prehistoric animals is based on chemical tracers in the fossils themselves. This direct evidence provides a different perspective than those based on comparative morphology of fossils, or circumstantial evidence from abundances of fauna or sediments. We measured carbon isotope (13C/12C), strontium isotope (87Sr/86Sr), and trace element (Sr/Ca) ratios in enamel and bone of fossil hominids and the associated fauna at Swartkrans. Using results from a large suite of fauna as a framework, we find that 13C/12C for both Paranthropus and Homo indicate the incorporation of a small but significant contribution from C4 grass, probably in the form of grass-eating animals, while Sr/Ca values fall in between those typical for herbivores and carnivores. These results are most consistent with omnivory, providing a new view of Paranthropus diets and raising questions about the extent of niche separation between this species and Homo. Faunal 13C/12C values indicate the dominance of C4 grassland at that time, consistent with interpretations derived from faunal abundances. 87Sr/86Sr ratios in fossils hold promise as habitat indicators since values in the environment and foodweb are generally directly derived from the local geology. Differences detected in the fossils may be used either as a riverine niche-indicator, or for the detection of immigrants from geologically different areas.