The Australian sea lion, Neophoca cinerea is an endangered pinniped species (IUCN Red List, 2008) occupying an upper trophic level within the marine ecosystem. As such, it is a useful indicator species of trace element and heavy metal (toxicant) concentrations. Anthropogenic sources of toxicants when at high concentrations can be associated with increased susceptibility to disease, mortality and reduced reproductive success. A specific objective of the recovery plan for N. cinerea is to investigate and mitigate potential threats, including pollutant exposure. In a population significantly impacted by endemic disease due to the intestinal nematode hookworm, investigating toxicant concentrations and their role in increasing susceptibility and severity of disease outcomes, is paramount. ICP-MS was used to determine the concentration of 13 elements, Hg, Pb, As, Se, Cd, Mg, Al, Co, Ni, Cu, Zn, Cr, and Fe in liver and hair samples collected from N. cinerea pups sampled at two South Australian colonies from 2006 to 2013. The concentration of mercury (Hg) in both liver (mean = 28.9 μg/g drywt; n=39) and hair (mean = 5.4 μg/g drywt; n = 199) were among some of the highest reported in pinnipeds and were associated with an increased age at which pups shed hookworm infection and reduced health status, likely due in part to the immunosuppressive effects of Hg. Toxicant concentrations, particularly Hg, are likely a significant risk factor for hookworm disease in N. cinerea pups. As such, monitoring toxicant concentrations is important for the conservation and management of this endangered species.