ABSTRACT: Vulnerable marine ecosystems, including deep-sea corals and sponges, are important habitats for many fish and invertebrate species and are at risk from the effects of fishing, seafloor mining, and climate change. We describe the zoogeography of deep-sea corals and sponges in Alaska, USA, and identify the environmental factors structuring these assemblages. Images were collected with a calibrated stereo drop-camera (n = 853 transect locations). We used cluster analysis to identify assemblages, canonical correspondence analysis to identify the primary environmental variables structuring these assemblages, and random forest and generalized additive modeling to predict their spatial distributions. The 6 identified assemblages were well defined with each dominated by a single indicator taxon (2 coral taxa: Primnoidae, Stylasteridae; 2 sponge taxa: Demosponge, Hexactinellid; 2 sea whip/pen taxa: Balticina sp., Ptilosarcus gurneyi). The most common assemblages were Demosponge, Primnoidae and Balticina sp. Primnoidae and Demosponge were positively influenced by greater maximum tidal current, bottom current and bottom temperature as well as proportion of rock and cobble (high for Primnoidae and low to medium for Demosponge). Balticina sp. was influenced in the opposite direction and was aligned along lower maximum tidal current, bottom current, and bottom temperature as well as unconsolidated sediment and greater depth. We defined vulnerable marine ecosystem (VME) community indicators as the 6 assemblages each dominated by a single indicator taxa. These VME community indicators can guide identification of protected areas.