The depletion of shallow-water fish stocks through overexploitation has led to increasing fishing pressure on deep-sea species. Poor knowledge of the biology of commercially valuable deep-water fish has led to the serial depletion of stocks of several species across the world. Data regarding the genetic structure of deep-sea fish populations is important in determining the impact of overfishing on the overall genetic variability of species and can be used to estimate the likelihood of recolonisation of damaged populations through immigration of individuals from distant localities. Here the genetic structure of the commercially fished deep-water species the blackspot sea bream, Pagellus bogaraveo is investigated in the northeastern Atlantic using partial DNA sequencing of mitochondrial cytochrome b (cyt-b) and D-loop regions and genotyping of microsatellite loci. An absence of variation in cyt-b and low genetic variation in D-loop sequences potentially indicate that P. bogaraveo may have undergone a severe bottleneck in the past. Similar bottlenecks have been detected in other Atlantic species of fish and have possibly originated from the last glaciation. P. bogaraveo may have been particularly vulnerable to the effects of low temperature and a fall in sea level because stages of its life history occur in shallow water and coastal sites. However, there are other explanations of low genetic variability in populations of P. bogaraveo, such as a low population size and the impacts of fishing on population structure. Analysis of population structure using both D-loop and microsatellite analysis indicates low to moderate, but significant, genetic differentiation between populations at a regional level. This study supports studies on other deep-sea fish species that indicate that hydrographic or topographic barriers prevent dispersal of adults and/or larvae between populations at regional and oceanographic scales. The implications for the management and conservation of deep-sea fish populations are discussed.