Abstract Background Emerging global positioning system (GPS) technologies can clarify movement patterns of free-ranging animals in far more detail than has been possible with previous methods. We conducted long-term (mean, 65 days; maximum, 221 days) GPS radio-tracking of 41 northern bluetongue lizards (Tiliqua scincoides intermedia) and 8 centralian bluetongue lizards (T. multifasciata) at two study sites in northwestern Australia, close to the border between Western Australia and the Northern Territory. Results Individuals of both species spent long periods within small and distinctive habitat patches, interspersed with longer directional relocations from one patch to the next. Our sampling showed that these patches of core activity differed significantly from the surrounding landscape in several respects. The patches provided relatively shaded, cool, and damp conditions, with higher grass and more leaf-litter cover. The location of these patches in the landscape is probably determined by drainage patterns, soil moisture-holding ability, and stochastic recruitment of shade trees. Conclusions These scattered patches provide a critically important habitat for lizards (and probably, other taxa) within this hot dry landscape. Future conservation and management strategies need to prioritize the retention of such sites, at a spatial scale that allows animals to move between them.