The Arctic Ocean is undergoing major changes in many of its fundamental physical constituents, from a shift from multi- to first-year ice, shorter ice-covered periods, increasing freshwater runoff and surface stratification, to warming and alteration in the distribution of water masses. These changes have important impacts on the chemical and biological processes that are at the root of marine food webs, influencing their structure, function and biodiversity. Here we summarise current knowledge on the biodiversity of Arctic marine ecosystems and provide an overview of fundamental factors that structure ecosystem biodiversity in the Arctic Ocean. We also discuss climate-associated effects on the biodiversity of Arctic marine ecosystems and discuss implications for the functioning of Arctic marine food webs. Based on the complexity and regional character of Arctic ecosystem reponses to environmental changes, recommendations are made for the establishment of long-term observatories across the Arctic, in support of sustainable management and conservation actions.