A genetic study to determine the population structure of minke whales Balaenoptera acutorostrata in Greenland, the Central and NE Atlantic and the North Sea was carried out on a sample of 306 individuals. Samples were analysed by sequencing the D-loop in mtDNA and using 16 polymorphic nuclear microsatellite markers. Muscle samples from a total of 154 minke whales, caught between 6 May and 31. October 1998 by Greenland and Norwegian licensed whalers within 6 areas of the North Atlantic, were analysed (West Greenland, n = 44; Jan Mayen, n = 24; Svalbard, n = 16; the Barents Sea, n = 33; Vesteralen/Lofoten on the coast of northwestern Norway, n = 14, and the North Sea, n = 23). In addition, 30 minke whales sampled in East Greenland during 1996, 1997 and 1999 were included. Furthermore, 122 minke whales caught in West Greenland in 3 different years (1982, 1996 and 1997) were analysed to determine potential inter-annual variation within a sampling area. The lack of inter-annual variation in West Greenland suggests that the minke whales summering in the area year after year belong to the same sub-population. The study indicated the existence of 4 genetically differentiated sub-populations: (1) West Greenland, (2) Central North Atlantic-East Greenland-Jan Mayen area, (3) NE Atlantic (Svalbard, the Barents Sea and northwestern Norway), and (4) North Sea. It is suggested that these sub-populations have been isolated by discontinuities between regions, i.e. each of the sub-populations has evolved in response to regional differences in ecological conditions (oceanography, ice cover, prey type and prey availability).