Phylogeographic studies of eastern Australia have generally supported earlier biogeographical studies based on taxon distributions by concurring in the placement of significant intraspecific boundaries. Such studies may potentially clarify biogeographic boundaries that are presently unclear, such as the poorly defined southern edges of the McPherson Macleay Overlap. Here we investigate reptile phylogeography in the northern tablelands of New South Wales to study the south-western boundaries of the Overlap as these are especially uncertain. Cytochrome b sequences from Ctenotus robustus, C. taeniolatus and Oedura lesueurii, three lizard species widespread across the New England Tablelands, were analysed by examining single-strand conformational polymorphism and DNA sequencing. In both O. lesueurii and C. taeniolatus most deeper nodes within species define geographically localised clades. This was not the case for C. robustus. Boundaries between sister-group clades were discovered in multiple locations in the region – between Glen Innes and Armidale, between Armidale and Tamworth and to the south of the Liverpool Plains. The boundaries in C. taeniolatus and O. lesueurii were probably formed in at least two different periods. The phylogeographic patterns may be partly explained by glacially induced aridity cycles in the early Pleistocene or before.