We estimated the spatial population connectivity of Etelis carbunculus and E. coruscans based on measures of population genetic structure using the mitochondrial DNA control region. We collected samples from three areas separated by a minimum of 200 km around New Caledonia. We identified two separate genetic groups for E. carbunculus and a single group for E. coruscans. There were many singleton haplotypes distributed among geographic regions, indicating minimal spatial differentiation in genetic structure between regions for each species, although one of the genetic groups for E. carbunculus was in only two of the three regions. Conservation and management directives should consider both species as a single genetic stock among these three widespread regions. Our results provide evidence that stock structure might be less variable in the South Pacific than reported elsewhere, possibly indicating that trans-boundary management may be required in this region for deep-water snapper fisheries. Further refinement (including taxonomy) is required for E. carbunculus to characterize the different lineages observed.