Because of its remoteness and mid-latitude position, New Zealand lacks access to the tropical climates that might have ensured straightforward survival for frost-sensitive species during glacial times. Nevertheless, the New Zealand lowland flora retains a substantial complement of plants sourced in the tropics. While there have been extinction pulses for elements of the frost-sensitive flora under glacial/stadial regimes, the surviving remnants have been able to recolonize large areas of habitat during successive warm climate periods. Refugia for such species in stadial New Zealand are likely to have been localized and ecologically suboptimal. To examine these relationships we have applied chloroplast DNA sequence data to the investigation of phylogeographical pattern for five endemic species of Metrosideros subg. Metrosideros, a wide-ranging group of mostly frost-sensitive woody plants in New Zealand. The results of this research verify the location of two generally mooted stadial refugia for the country and provide support for the existence of a third. A simple pattern of chloroplast haplotype diversity was recorded in extra-refugial areas, compared with a greater complexity in the vicinity of the identified refugia. This pattern was independently repeated in both main islands. The proposed refugia correspond to contemporary localities of high average winter temperatures. The sharing of chloroplast haplotypes between the different species of Metrosideros examined suggests that there has been a history of repeated hybridization and introgression for these plants, possibly initiated by periods of refugial confinement. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 83, 399–412.