Studies using climatic gradients play a key role in our understanding of the importance of rainfall and temperature as factors regulating species diversity and distribution, and thus of likely responses to climate change. However, such studies currently consider above-ground species only, ignoring the diverse hypogaeic (subterranean) invertebrate fauna. Here, we assess the extent to which the responses of hypogaeic ant assemblages to a rainfall gradient in the Australian seasonal tropics are congruent with those of epigaeic (ground-dwelling) assemblages. We sampled at 20 sites covering a gradient of over 1000 km and 1100 mm in mean annual rainfall (MAR). We predicted that the different assemblages would display contrasting patterns because the epigaeic fauna is highly arid-adapted whereas the hypogaeic fauna is mesic-adapted in Australian savannas. We collected 392 epigaeic and 17 hypogaeic species. Epigaeic ant abundance and species diversity tended to increase with decreasing rainfall, whereas the reverse was shown by hypogaeic species. In contrast, the phylogenetic diversity (PD) of both epigaeic and hypogaeic assemblages showed only weak or no variation with rainfall. The low response of PD reflected the fact that additional species tended to come from the same rather than additional genera: genus-level diversity did not change with MAR. Epigaeic species composition formed three distinct clusters, corresponding to low, moderate and high MAR, whereas hypogaeic ants did not. Our findings show that ant assemblages can have stratum-specific responses to climatic gradients, reflecting different evolutionary histories of their constituent taxa. This may be true for other taxa, and has important implications for predicting responses to climate change. Lastly, we also show that different levels and facets of diversity have contrasting responses to climatic gradients. We thus advocate for ecological research simultaneously assessing assemblages of several strata, as well as varying levels and facets of their diversity.