There have been comparatively few large-scale studies on spatial genetic structure of bathyal seafloor fauna, despite the importance of these data to the successful management of the world's oceans. We use a comparative analysis of mitochondrial DNA from five bathyal (200–3500 m) species of brittle-stars (Ophiuroidea) to assess phylogeographic structure along an extensive (8000 km) longitudinal gradient at temperate latitudes (28–56°S) from south-west Australia (113°E) to seamounts east of New Zealand (175°W). We found no evidence of a genetic discontinuity between Australia and New Zealand, either across the temperate Tasman Sea or across the Southern Ocean between the South Tasman Rise and the Macquarie Ridge. However, there were latitudinal phylogeographical breaks between tropical, temperate and polar regions; longitudinal breaks across the eastern Indian Ocean; and a bathymetric break at approximately 1700 m. Although there was limited regional structure in the frequency of haplotype distributions within the major clades, and no clade appeared to be strictly panmictic, the regional structure in general was not concordant with a simple isolation-by-distance model. Demographic structure varied with three clades having a simplified haplotype network, low effective population sizes and no evidence of significant population expansion, and two clades having a high diversity of haplotypes, relatively high effective population sizes and signs of recent population expansion. These results are discussed with respect to putative dispersal strategies. We hypothesise that the ‘brooding’ species produce both brooded young and pelagic larvae, allowing for both the maintenance of local populations and long-distance dispersal.