Analyses of phylogeographic and population genetic structure of marine species with large population sizes, low fecundity, larval brooding, and limited dispersal such as the New Zealand flat oyster, Ostrea chilensis Küster, 1844, permit testing of the effects of historical and contemporary processes affecting patterns of coastal genetic differentiation and diversity. Analyses of DNA sequences from two mitochondrial DNA regions (COI, Cyt-b) compiled from O. chilensis individuals from 14 localities revealed a pronounced structure with three genetic clusters [Hauraki Gulf (HG); North; South] being resolved. These results suggest that historical processes have contributed to patterns of regional separation that have in turn contributed to regional genetic differences that are still observable today. Divergence time estimates of HG from North+South (1.97 Ma) and of North from South (0.36 Ma) indicate that O. chilensis from these regions represent evolutionarily significant units that evolved separately and rapidly in the early to middle Pleistocene. Analyses revealed no obvious periods of population expansion within any of the regions. These results contribute to a better understanding of how historical factors can result in pronounced mitochondrial DNA patterns of contemporary genetic structure and show how key life-history characteristics, e.g., larval brooding, can contribute to phylogeographic structure in coastal marine invertebrates.