The minke whale is the last of the great whale species to be hunted in significant numbers. Effective management must include an understanding of how genetic diversity is divided and distributed among putative local populations, and as for many migratory species, this is complicated for the minke whale by large-scale seasonal movement among geographic regions. The problem is that the geographic identity of breeding populations is not known, and instead these whales are predictably found and hunted where different breeding stocks may mix on seasonal feeding grounds. Here we use microsatellite DNA and mtDNA markers to investigate minke whale population structure across the species’ range in the North Atlantic. We found no evidence of geographic structure comparing putative populations in recognized management areas, though some limited structure had been indicated in earlier studies. However, using individual genotypes and likelihood assignment methods, we identified two putative cryptic stocks distributed across the North Atlantic in similar proportions in different regions. Some differences in the proportional representation of these populations may explain some of the apparent differentiation between regions detected previously. The implication would be that minke whales range extensively across the North Atlantic seasonally, but segregate to some extent on at least two breeding grounds. This means that established stock boundaries in the North Atlantic, currently used for management, should be re-considered to ensure the effective conservation of genetic diversity.