The spawning stock of Atlantic cod Gadus morhua in West Greenland waters was characterized by a drastic decline in the late 1960s and has since exhibited considerable variation. It has been suggested that the cod stock in West Greenland waters is composed of several stock components that include (1) a number of distinct local inshore populations spawning in separate fjord systems, (2) an offshore spawning component located on the fishing banks, and (3) a periodic Icelandic–East Greenland cod influx that mixes with the offshore and inshore West Greenland stock components. In an attempt to clarify the status of Atlantic cod in Greenland waters, we investigated the genetic structure at different inshore and offshore feeding grounds east and west of Greenland. A total of 1,581 genetic samples were collected within North Atlantic Fisheries Organization areas at inshore and offshore locations as well as within the International Council for the Exploration of the Sea area XIVb. Those samples were genotyped for 18 microsatellite loci and the pantophysin (Pan I) locus. Both types of genetic markers gave congruent results and suggest the presence of two distinct genetic components with limited connectivity in Greenland waters, namely, an inshore component and an offshore component.