Under the apparent homogeneity of soft-bottom ecosystems hides an heterogeneity of habitats driven by variations in sediment composition and environmental conditions. Using an extensive underwater video survey dataset, we explored the taxonomic diversity of soft-bottom Nephrops fishing grounds and their environmental drivers on a large latitudinal scale from the Bay of Biscay to the Irish Sea (Northeast Atlantic). Biogeographical network clustering highlighted indicator species of the different communities and a Between-Class Analysis characterised the abiotic factors influencing each community. Our analyses confirmed a biogeographical limit between the Bay of Biscay and the northern areas driven by a latitudinal temperature gradient and highlighting the distribution of Lusitanian and Boreal species. Mobile fish and crustaceans, and sessile filter-feeder assemblages differed along a depth, bottom current and fishing gradient. Some species assemblages covered the whole latitudinal range, implying a greater influence of optimal environmental surroundings rather than their geographical position. Vulnerable Marine Ecosystem indicator taxa such as Virgularia mirabilis and Pennatula phosphorea are potential indicator species of some clusters, while harvested species such as Nephrops norvegicus or mobile fish characterized other bioregions. Spatial knowledge produced in this study could be integrated as biodiversity layers together with fisheries activities layers in decision support tools such as Marine Spatial Planning in order to define compromise between conservational and fishing objectives. Outcomes of management scenarios would then consider the whole species stock (e.g. Nephrops) rather that local populations independently.