Persistent organic pollutants (POPs) cause toxicity effects in a wide range of species. Species dominating the upper trophic level are particularly vulnerable to bioaccumulative toxic effects caused by environmental pollutants. An alopecia syndrome has been recognised at high prevalence (up to 50% of juvenile females) in Australian fur seals, Arctocephalus pusillus doriferus, at Lady Julia Percy Island (LJP), Victoria. Previous investigations suggest causality could be due to a pollutant acting as an endocrine analogue. The alopecic syndrome is a likely risk factor for juvenile mortality. To investigate whether POPs are associated with endocrine disruption and alopecia, we compare POP’s concentration in the fur of alopecic (n=50) and non-alopecic (n=51) juvenile seals sampled at LJP, in fur collected from pups at LJP and three other colonies in Victoria and Tasmania (considered baseline colonies for comparison), and in blubber and fur samples collected from stranded fur seals in Victoria. The concentration of selected POPs including dioxin/furans (PCDD/Fs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs) and perfluoralkyl compounds was determined using high resolution mass spectrometry or liquid chromatography-mass spectrometry. High levels of several POPs, including dioxins, were detected, indicating that pinniped pups are at risk of POPs mediated toxicity in-utero, at a particularly susceptible developmental stage. We discuss the significance of POPs concentrations in relation to the causality of alopecia and the conservation management of the marine ecosystem, and assess the usefulness of fur as a non-invasive biomarker to assess POPs exposure in this sentinel species.