Alaskan Arctic shelf communities are currently experiencing dramatic changes that will likely affect ecosystem functioning of Arctic marine benthic communities. Here, functional diversity based on biological traits was used to assess differences and similarities in ecosystem functioning between 2 shelf systems that are geographically close but vary in many environmental influences: the Arctic Beaufort and Chukchi Sea epibenthic communities. We hypothesized that (1) patterns of functional composition and diversity metrics reflect patterns in taxonomic composition and diversity metrics in these 2 shelf communities; and (2) patterns in functional diversity metrics are distinct between the 2 shelves. We evaluated 9 biological traits (body form, body size, feeding habit, fragility, larval development, living habit, movement, reproductive strategy, sociability) for 327 taxa in 2014 and 2015. For each trait, multiple modalities (specific expressions within a trait) were considered. Patterns in functional diversity metrics on both shelves reflected those in taxonomic diversity metrics. However, shelf communities were more similar in functional- than in taxonomic composition. Beaufort Sea communities had higher functional dissimilarity and functional evenness driven by differences in the modalities within body form, body size, larval development, and reproductive strategy. These traits primarily affect nutrient cycling, energy turnover, and recovery from disturbances, suggesting a stronger potential for future maintenance of ecosystem function, and indicating a more even use of resources in the Beaufort Sea. The combination of functional and taxonomic diversity metrics enabled a comprehensive understanding of how ecological niche space is used and how epibenthic communities function in Alaskan Arctic shelf systems.