A prominent feature of New Zealand biogeography is that species endemicity and diversity is not evenly distributed but shows an alternating pattern of latitudinal variation. Endemicity is generally highest in South Island and northern North Island and low in southern North Island. A prominent landscape feature that is partly correlated with this is Cook Strait, which separates the two main islands of New Zealand and marks the southern boundary of a region that interests biogeographers and geologists alike. This region encompasses a zone of intense tectonic strain related to the transfer of plate convergence via subduction into oblique-slip and strike-slip faulting. We review geological information and provide new palaeogeographic reconstructions of the area that depict changes in the distribution of mountains, the extent to which southern North Island was under the ocean, and the history of marine straits over the last 4 million years. This information is essential for the development of testable biogeographic hypotheses. We find that the Wellington region was formerly connected to the relatively mountainous Marlborough area, and more distant than today from the northern island of the time. Significant topography in the Kaimanawa Range is probably of Early Pliocene age. However, the Ruahine-Tararua ranges and Taranaki-Taupo volcanics have formed since c. 1 Ma. The implications for the biogeography of central New Zealand are considerable in terms of habitat availability for establishment of terrestrial species and opportunities for range shifting of both terrestrial and coastal organisms.