Phylogeographic studies frequently reveal multiple morphologically-cryptic lineages within species. What is yet unclear is whether such lineages represent nascent species or evolutionary ephemera. To address this question, we compare five contact zones, each of which occurs between eco-morphologically cryptic lineages of rainforest skinks from the rainforests of the Australian Wet Tropics. Although the contacts likely formed concurrently in response to Holocene expansion from glacial refugia, we estimate that the divergence times (t) of the lineage-pairs range from 3.1 to 11.5 Myr. Multilocus analyses of the contact zones yielded estimates of reproductive isolation that are tightly correlated with divergence time and, for longer-diverged lineages (t > 5 Myr), substantial. These results show that phylogeographic splits of increasing depth can represent stages along the speciation continuum, even in the absence of overt change in ecologically relevant morphology.