A model of the metapopulation structure of narwhals Monodon monoceros in Baffin Bay, Hudson Bay and adjacent waters is proposed based on satellite telemetry data collected over two decades from six coastal aggregations of narwhals in the eastern Canadian high Arctic, Hudson Bay and West Greenland. In addition, data on seasonal catches of narwhals in 11 Inuit communities are used to provide information on the occurrence of narwhals. The tracking data suggest that disjunct summer aggregations of narwhals are, to some extent, demographically independent subpopulations, with minimal or no exchange with other summering aggregations. We propose that these should be considered separate stocks for management purposes. Year-round satellite tracking of individuals demonstrates that whales return to the same summering areas the following year, suggesting inter-annual site fidelity. We propose that the narwhals in Canada constitute five separate stocks, with limited exchange between three of the stocks. Coastal summer aggregations in Greenland constitute two stocks in addition to two fall and winter aggregations supplied by narwhals from several summering areas. Several narwhal stocks mix on the wintering areas in Baffin Bay, but the metapopulation structure is likely maintained through a combination of life-history traits and migratory routes, as mating most likely occurs after the initiation of the return migration toward summering areas. The metapopulation structure in Baffin Bay narwhals will be impacted differentially by Inuit subsistence hunting, depending on the migratory schedule of narwhals and dates at which whales occur in different seasonal hunting areas. It is therefore important to identify which narwhal stocks contribute to which subsistence hunts in order to assess the sustainability of those hunts. This paper proposes a preliminary stock model for this purpose.