The island of New Guinea lies in one of the most tectonically active regions in the world and has long provided outstanding opportunity for studies of biogeography. Several chelid turtles, of clear Gondwanal origin, occur in New Guinea; all species except one, the endemic Elseya novaeguineae, are restricted to the lowlands south of the Central Ranges. Elseya novaeguineae is found throughout New Guinea. We use mitochondrial and nuclear gene variation among populations of E.novaeguineae throughout its range to test hypotheses of recent extensive dispersal versus more ancient persistence in New Guinea. Its genetic structure bears the signature of Miocene vicariance events. The date of the divergence between a Birds Head (Kepala Burung) clade and clades north and south of the Central Ranges is estimated to be 19.8Mya [95% highest posterior density (HPD) interval of 13.3-26.8Mya] and the date between the northern and southern clades is estimated to be slightly more recent at 17.4Mya (95% HPD interval of 11.0-24.5Mya). The distribution of this endemic species is best explained by persistent occupation (or early invasion and dispersal) and subsequent isolation initiated by the dramatic landform changes that were part of the Miocene history of the island of New Guinea, rather than as a response to the contemporary landscape of an exceptionally effective disperser. The driving influence on genetic structure appears to have been isolation arising from a combination of: (1) the early uplift of the Central Ranges and establishment of a north-south drainage divide; (2) development of the Langguru Fold Belt; (3) the opening of Cenderawasih Bay; and (4) the deep waters of the Aru Trough and Cenderawasih Bay that come close to the current coastline to maintain isolation of the Birds Head through periods of sea level minima (-135m). The dates of divergence of turtle populations north and south of the ranges predate the telescopic uplift of the central ranges associated with oblique subduction of the Australian Plate beneath the Pacific Plate. Their isolation was probably associated with earlier uplift and drainage isolation driven by the accretion of island terranes to the northern boundary of the Australian craton that occurred earlier than the oblique subduction. The opening of Cenderawasih Bay is too recent (6 Mya) to have initiated the isolation of the Birds Head populations from those of the remainder of New Guinea, although its deep waters will have served to sustain the isolation through successive sea level changes. The molecular evidence suggests that the Birds Head docked with New Guinea some time before the Central Ranges emerged as a barrier to turtle dispersal. Overall, deep genetic structure of the species complex reflects events and processes that occurred during Miocene, whereas structure within each clade across the New Guinea landscape relates to Pliocene and Pleistocene times.