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In pelagic species inhabiting large oceans, genetic differentiation tends to be mild and populations devoid of structure. However, large cetaceans have provided many examples of structuring. Here we investigate whether the sperm whale, a pelagic species with large population sizes and reputedly highly mobile, shows indication of structuring in the eastern North Atlantic, an ocean basin in which a single population is believed to occur. To do so, we examined stable isotope values in sequential growth layer groups of teeth from individuals sampled in Denmark and NW Spain. In each layer we measured oxygen-isotope ratios (delta O-18) in the inorganic component (hydroxyapatite), and nitrogen and carbon isotope ratios (delta N-15: delta C-13) in the organic component (primarily collagenous). We found significant differences between Denmark and NW Spain in delta N-15 and delta O-18 values in the layer deposited at age 3, considered to be the one best representing the baseline of the breeding ground, in delta N-15, delta C-13 and delta O-18 values in the period up to age 20, and in the ontogenetic variation of delta N-15 and delta O-18 values. These differences evidence that diet composition, use of habitat and/or migratory destinations are dissimilar between whales from the two regions and suggest that the North Atlantic population of sperm whales is more structured than traditionally accepted.