Understanding the ecological processes that shape spatial genetic patterns of population structure is critical for understanding evolutionary dynamics and defining significant evolutionary and management units in the deep sea. Here, the role of environmental factors (topographic, physico-chemical and biological) in shaping the population genetic structure of four deep-sea habitat-forming species (one sponge -Poecillastra laminaris, three corals -Goniocorella dumosa, Madrepora oculata, Solenosmilia variabilis) was investigated using seascape genetics. Genetic data (nuclear and mitochondrial sequences and microsatellite multilocus genotypes) and environmental variables were employed to build individual-based and population-level models. The results indicated that environmental factors affected genetic variation differently amongst the species, as well as at different geographic scales. For individual-based analyses, different environmental variables explained genetic variation in P. laminaris (dissolved oxygen), G. dumosa (dynamic topography), M. oculata (sea surface temperature and surface water primary productivity), and S. variabilis (tidal current speed). At the population level, factors related to current and food source explained the regional genetic structure in all four species, whilst at the geomorphic features level, factors related to food source and topography were most important. Environmental variation in these parameters may be acting as barriers to gene flow at different scales. This study highlights the utility of seascape genetic studies to better understand the processes shaping the genetic structure of organisms, and to identify environmental factors that can be used to locate sites for the protection of deep-sea Vulnerable Marine Ecosystems.How spatially variable environmental and habitat features influence evolutionary processes and population genetic connectivity in the deep sea is poorly understood 1-3 . The deep-sea environment experiences increasing pressure, decreasing pH, and generally decreasing temperature, with increasing depth 4 . Such single factor or multi-factorial gradients may strongly influence dispersal, settlement and recruitment patterns of deep-sea taxa 5-7 . Additionally, features such as bottom currents 8 , surface currents 9 and bathymetry may play important roles in shaping the patterns of genetic connectivity amongst populations in many deep-sea species 5,10,11 , with the result that multiple environmental factors may act as barriers to or promoters of gene flow in the deep sea 8,9,12 and thereby strongly influence population genetic structure at different spatial and even temporal scales. However, the complexity of the deep-sea physico-chemical environment and the logistical difficulties of sampling (both biological specimens and environmental data) such a large biome have limited our ability to understand multispecies patterns of population genetic structure and how these are influenced by environmental variation 3,13-15 .Deep-sea vulnerable marine ecosystems (VMEs) ...