Harbour seals and harbour porpoises are top predator species from the North Sea, have long life spans and hence, are known to accumulate high levels of anthropogenic contaminants. To gain knowledge about the behaviour of naturally-produced compounds in these marine mammals, the biomagnification of naturally-produced methoxylated polybrominated diphenyl ethers (MeO-PBDEs) was assessed. The biomagnification of MeO-PBDEs (2'-MeO-BDE 68 and 6-MeO-BDE 47) was lower in harbour seals (all biomagnification factors (BMFs)<1) compared to the same age-gender groups of the harbour porpoises (all BMFs>1). This may indicate a better metabolic breakdown of MeO-PBDEs in harbour seals, as was previously suggested for polybrominated diphenyl ethers (PBDEs). In both predators, 6-MeO-BDE 47 had the highest concentrations (range: 45-483 ng/g lw and 2-38 ng/g lw for harbour porpoises and seals, respectively) compared to 2'-MeO-BDE 68 (range: 2-28 ng/g lw and 1-6 ng/g lw for harbour porpoises and seals, respectively). In general, the highest concentrations were found in juveniles, suggesting an increased biotransformation capacity with age or the influence of dilution by growth for both species. Here we show that naturally-produced brominated organic compounds can biomagnify and accumulate in North Sea top predators, although to a lesser extent than anthropogenic lipophilic contaminants, such as polychlorinated biphenyls (PCBs) or PBDEs.