There is newly invigorated interest in intensifying agriculture in northern Australia, and research has identified up to 17 M ha of suitable soils, much of which are floodplains. Given that 88% of these best soils for agriculture occur outside the current protected area network, and floodplains are a minority habitat in northern Australia, developing northern Australia whilst maintaining its biodiversity will be a great challenge. Ants are a particularly prominent and diverse faunal group within northern Australia, but almost nothing is known of the floodplain fauna. We sampled 20 pairs of plots in floodplains and surrounding savannas in three locations in the high rainfall zone of the Northern Territory to investigate the ant faunal composition of the floodplains, to determine to what extent they are comprised of species unique to floodplains or just a subset of the broader savanna fauna. We collected 114 species from 29 genera. Eighteen species were found only in floodplain plots, but only three were definitively floodplain specialists and another four had a propensity for clay soils. For all locations combined, savanna plots contained approximately 1.7 times more species than floodplain plots. Multivariate analysis found that the two habitats supported distinct ant faunas and the three locations also had distinct faunas. Nine species in this study were new to science, suggesting that there are many other species yet to be discovered. The results indicate that floodplains have conservation value for ant biodiversity, as is the case for other components of the biota. Efforts to intensify agriculture on north Australian floodplains therefore need to have effective conservation considerations if we are to achieve ecologically sustainable development.