Benthic communities and their activity are important to ecosystem processes in the polar marine environment. Benthic diversity and production feeds into higher levels of the food chain, benthic remineralization returns nutrients into the water column usable for primary production, and sponge and deep sea coral beds provide structural complexity to habitats and host many associated species. Given the limited spatial coverage of benthic sampling, proxies such as sediment pigment concentration, strong topographic features and polynyas can be used as indicators for benthic production. We used the density of coral and sponge beds, benthic diversity and biomass, benthic remineralization and sediment pigment concentration to identify benthic ecologically and biologically significant areas (EBSA)s in the Canadian Arctic for the Hudson Bay Complex, Eastern Arctic and Western Arctic biogeographic regions. Areas of Hudson Strait have relatively high concentrations of soft corals and sponges compared to other areas within the Hudson Bay Complex, while Baffin Bay-Davis Strait areas in the Eastern Arctic are characterized by large aggregations of sea pens, large gorgonian corals and sponges. In Baffin Bay, particularly important populations of Pennatulacean sea pens are found at the outflow of Lancaster Sound and along the continental slope off Baffin Island. In Davis Strait particularly abundant beds of large gorgonian coral and sponges are found in the Hatton Basin (outflow of Hudson Strait). The Narwhal over-wintering site in Davis Strait has large aggregations of gorgonian corals as well as the rarer black corals. Lancaster Sound and the North Water Polynya areas support high benthic diversity, benthic biomass and high benthic boundary fluxes, as well as still undescribed species such as rare species of enteropneusts. Both polynyas and strong current zones are indicative of high benthic diversity and activity in the Western Arctic, more specifically in Victoria Strait and Franklin Strait. In the Beaufort Sea LOMA, additional benthic EBSAs are suggested in Franklin Bay and the Prince of Wales Strait. There is a large deficiency of data in the Arctic Basin and Canadian Arctic Archipelago, but presence of polynyas in those regions may serve as a proxy of high benthic biodiversity and productivity.