The palaeoecology of the coeval Middle Triassic non-mammalian cynodonts, Diademodon and Cynognathus (Therapsida) remains poorly understood although their gross morphology has been studied intensively. Significant differences in their growth patterns suggest inherent biological differences, despite having inhabited similar environments. In this study, the palaeoecology of Cynognathus and Diademodon specimens were examined using intra-tooth stable carbon and oxygen isotope analyses of enamel carbonate. The resulting stable isotope patterns of Cynognathus and Diademodon were compared with that of Crocodylus niloticus and published mammalian tooth enamel data. Predictably, the non-mammalian cynodont δ 13C values fall within the expected range for C 3 plant diets. Both δ 18O and δ 13C values of Diademodon are markedly more depleted than those of Cynognathus, suggesting that the former fed in shadier, damper areas, was nocturnal and/or depended more directly on environmental water. The seasonal amplitude reflected in the Cynognathus teeth is relatively low. However, high amplitude, directional δ 18O intra-tooth variations in the Diademodon teeth are comparable to, or higher than, those observed for extant mammalian and C. niloticus teeth from semi-arid, seasonal regions. This suggests that marked seasonality prevailed in the Karoo Basin during the Middle Triassic, and that Diademodon was sensitive to these variations. These isotopic differences between Diademodon and Cynognathus indicate differing responses to climatic fluctuations and reveal new insights into the palaeoecology of non-mammalian cynodonts.