RATIONALEThe relationship between stocks of fin whales inhabiting the temperate eastern North Atlantic and the Mediterranean Sea is subject to controversy. The use of chemical markers facilitates an alternative insight into population structure and potential borders between stocks because the two areas present dissimilar isotopic baselines.METHODSBaleen plates, composed of inert tissue that keeps a permanent chronological record of the isotopic value of body circulating fluids, were used to investigate connectivity and boundaries between the stocks. Values were determined by continuous flow isotope ratio mass spectrometry.RESULTSStable isotopes confirm that, while the two subpopulations generally forage in well‐differentiated grounds, some individuals with characteristic Atlantic values do penetrate into the Mediterranean Sea up to the northernmost latitudes of the region. As a consequence, the border between the two putative subpopulations may be not as definite as previous acoustic investigations suggested. The discriminant function obtained in this study may assist researchers to use baleen plate isotopic data to assign the origin of fin whales of uncertain provenance.CONCLUSIONSThis study strengthens the stock subdivision currently accepted for management and conservation while recognizes a low level of exchange between the Mediterranean and temperate eastern North Atlantic subdivisions. Copyright © 2013 John Wiley & Sons, Ltd.