A combination of heavy metals, organochlorines (OC) and fatty acids (FA) that reflect long‐term deposition (1+ year) in tissues was used in a Canonical Discriminant Analysis (CDA) exploring population substructure in 104 minke whales Balaenoptera acutorostrata that were sampled in West Greenland, the Central and Northeast Atlantic Sea and in the North Sea in 1998. Using a CDA that included mercury and cadmium in muscle, liver and kidney, and eight OCs and four unsaturated FAs in blubber we were able to separate the whales into four subpopulations: 1) a West Greenland group, 2) a Central Atlantic group represented by whales from Jan Mayen, 3) a Northeast Atlantic group (Svalbard, Barents Sea and northwestern Norway), and 4) a North Sea group. During an assignment test based on the data transformation developed by the CDA, about 84% of the individuals were correctly assigned to the area where they had been caught. The highest degree of misassignment was between Jan Mayen and the Northeast Atlantic groups. The differences among the four groups likely reflected regional differences (i.e. sea water chemistry, prey type and prey availability) among the marine ecosystems within the range studied. The study indicated that a multi‐elemental approach based on long‐term deposited compounds with different ecological and physiological pathways can be used for identification of subpopulations of marine mammals.