Identification of ecologically significant units at different spatial scales is essential for management of biodiversity attributes. This case study illustrates a coupled methodological approach to delineate benthic habitats and associated assemblages at different spatial scales. Two complementary analyses were employed based on the occurrences of 99 epibenthic invertebrate species in Atlantic Canada, sampled during depth-stratified random trawl sets. To identify epibenthic assemblage types, isometric feature mapping and partitioning around medoids (ISOPAM) was used in combination with a joint species distribution model (JSDM), which also produced continuous distribution surfaces across the spatial domain. ISOPAM identified nine significantly spatially coherent assemblages (biotopes) at spatial scales of hundreds of meters to hundreds of kilometers, with associated diagnostic species. Those assemblages were closely matched by eight regions of common profile using the JSDM, indicating strong environmental influences on their distributions. These smaller-scale assemblages were grouped into three biophysical units. The results from the JSDM were validated with independent data showing good congruence. This indicates that the spatial units ascribed to identified assemblages are robust and suitable for marine spatial planning and monitoring.