The central Australian desert ant Melophorus bagoti lives in a visually cluttered semi-arid habitat dotted with grass tussocks, bushes and trees. Previously, it was shown that this species has a higher propensity to switch from vector-based navigation to landmark-guided navigation compared with the North African desert ant Cataglyphis fortis, which usually inhabits a visually bare habitat. Here, we asked whether different colonies of M. bagoti, inhabiting more and less cluttered habitats, show a similar difference. We compared ants from typically cluttered habitats with ants from an exceptional nest located in an open field largely devoid of vegetation. Ants from both kinds of nests were trained to forage from a feeder and were then displaced to a distant test site on the open field. Under these conditions, ants from cluttered habitats switched more readily from vector-based navigation to landmark-guided navigation than ants from the open field. Thus, intraspecific differences caused by the experience of particular landmarks encountered en route, or of particular habitats, influence navigational strategies in addition to previously found interspecific, inherited differences due to the evolutionary history of living in particular habitats.