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Aim The geology and hydrology of the Central Ranges of Australia provide refuge for more mesic-adapted taxa unable to survive in the surrounding deserts. Whether this area has been a long-term refuge for mesic-adapted taxa is uncertain. Mesic-adapted taxa in the region have been argued as 'relicts', remnants of wet forests once covering the region. This scenario hypothesizes that 'relicts' survived in pockets of moist habitat in the Central Ranges as the Australian arid zone expanded. Here, we test an hypothesis of long-term occupancy in the Central Ranges for a cycad, Macrozamia macdonnellii, a taxon of conservation concern and also one frequently described as an 'ancient relict'. Location Australia. Methods A haplotype network, derived from DNA sequences of two chloroplast regions, was used to infer the biogeographical history of Macrozamia across Australia. Specifically, the question of long-term occupancy of the Central Australian Ranges is addressed. Results Macrozamia macdonnellii shares a haplotype with five eastern species. However, unique haplotypes restricted to only a part of the Mac Donnell Ranges Interim Biogeographic Regionalisation of Australia region are also present. Western Australian species of Macrozamia form a lineage distinct from those in the rest of Australia. Main conclusions The shared haplotype, nested within haplotypes from eastern Australia, indicates that M. macdonnellii is relatively recently derived from ancestral lineages of eastern Australia. This starkly contrasts with species of Macrozamia in Western Australia, which show long-term isolation from those in the east. Unique haplotypes in populations of M. macdonnellii indicate that the species has occupied the region for sufficient time to accumulate variation. Furthermore, this variation appears to be geographically structured. If so, it indicates that M. macdonnellii is undergoing population differentiation, and possible speciation, in different regions of the Mac Donnell Ranges. Isolated populations with unique haplotypes might be evolutionarily significant units that should be conserved. [ABSTRACT FROM AUTHOR]