Lumpfish, or lumpsucker, Cyclopterus lumpus (Linnaeus, 1758) is widely distributed in the North Atlantic Ocean. It has a considerable economic value and substantial fisheries occur in several North Atlantic regions owing to the use of its fully ripe internal egg masses in the ovaries as an alternative to sturgeon caviar. Despite being intensively fished in several locations, biological knowledge is limited and no genetic structure information is available. In this study, the stock structure of C. lumpus was investigated across the North Atlantic using ten microsatellite loci. Out of ten loci, two exhibited higher level of differentiation but their inclusion/exclusion from the analyses did not drastically change the observed genetic pattern. A total of three distinct genetic groups were detected: Maine–Canada–Greenland, Iceland–Norway and Baltic Sea. These results, discussed in terms of origin of differentiation, gene flow, and selection, showed that gene flow was rather limited among the detected groups, and also between Greenland and Maine–Canada.