Invasive species can induce shifts in habitat use by native taxa: either by modifying habitat availability, or by repelling or attracting native species to the vicinity of the invader. The ongoing invasion of cane toads (Rhinella marina) through tropical Australia might affect native frogs by affecting refuge-site availability, because both frogs and toads frequently shelter by day in burrows. Our laboratory and field studies in the wet-dry tropics show that native frogs of at least three species (Litoria tornieri, Litoria nasuta and Litoria dahlii) preferentially aggregate with conspecifics, and with (some) other species of native frogs. However, the frogs rarely aggregated with cane toads either in outdoor arenas or in standardized experimental burrows that we monitored in the field. The native frogs that we tested either avoided burrows containing cane toads (or cane toad scent) or else ignored the stimulus (i.e. treated such a burrow in the same way as they did an empty burrow). Native frogs selected a highly non-random suite of burrows as diurnal retreat sites, whereas cane toads were less selective. Hence, even in the absence of toads, frogs do not use many of the burrows that are suitable for toads. The invasion of cane toads through tropical Australia is unlikely to have had a major impact on retreat-site availability for native frogs.