Polar bears (Ursus maritimus) are being impacted by climate change and increased exposure to pollutants throughout their northern circumpolar range. In this study, we quantified concentrations of total mercury (THg) in the hair of polar bears from Canadian high- (southern Beaufort Sea, SBS) and sub- (western Hudson Bay, WHB) Arctic populations. Concentrations of THg in polar bears from the SBS population (14.8 ± 6.6 μg g(-1)) were significantly higher than in polar bears from WHB (4.1 ± 1.0 μg g(-1)). On the basis of δ(15)N signatures in hair, in conjunction with published δ(15)N signatures in particulate organic matter and sediments, we estimated that the pelagic and benthic food webs in the SBS are ∼ 4.7 and ∼ 4.0 trophic levels long, whereas in WHB they are only ∼ 3.6 and ∼ 3.3 trophic levels long. Furthermore, the more depleted δ(13)C ratios in hair from SBS polar bears relative to those from WHB suggests that SBS polar bears feed on food webs that are relatively more pelagic (and longer), whereas polar bears from WHB feed on those that are relatively more benthic (and shorter). Food web length and structure accounted for ∼ 67% of the variation we found in THg concentrations among all polar bears across both populations. The regional difference in polar bear hair THg concentrations was also likely due to regional differences in water-column concentrations of methyl Hg (the toxic form of Hg that biomagnifies through food webs) available for bioaccumulation at the base of the food webs. For example, concentrations of methylated Hg at mid-depths in the marine water column of the northern Canadian Arctic Archipelago were 79.8 ± 37.3 pg L(-1), whereas, in HB, they averaged only 38.3 ± 16.6 pg L(-1). We conclude that a longer food web and higher pelagic concentrations of methylated Hg available to initiate bioaccumulation in the BS resulted in higher concentrations of THg in polar bears from the SBS region compared to those inhabiting the western coast of HB.