Genetic data were used as an indirect means of assessing connectivity among deep-sea coral populations on seamounts and slopes in the Australian and New Zealand region. We sequenced three DNA regions (16S, ITS and Control Region) in nine deep-sea coral species from sites spanning thousands of kilometers. Based on haplotype distributions and AMOVA, we found evidence of genetic subdivision across ocean expanses for three species: the scleractinian Desmophyllum dianthus, and the antipatharians Antipathes robillardi and Stichopathes variabilis. Levels of genetic variation were low for the remaining species, including the reef-forming Solenosmila variablis and Madrepora oculata, and more sensitive molecular markers may be needed to resolve their spatial structure properly. For two species (the scleractinian Stephanocyathus spiniger and the antipatharian Stichopathes filiformis), we found no evidence of genetic subdivision among sites within regions, suggesting sufficient gene flow occurs to maintain genetic homogeneity at scales of tens to hundreds of kilometers. Recognising that some seamount regions and coral populations are, or are not, effectively isolated will be a key component of successful management planning based on marine protected area networks – both within and beyond national jurisdictions.