While mercury is a natural element, it is also a pollutant of global concern and is released by both natural processes (e.g. volcanism) and anthropogenic activities (e.g. gold mining). Anthropogenic mercury emissions are predicted to increase over time with growing industrialisation and can travel over vast distances. The polar regions are known sinks for mercury owing to their unique environmental conditions that facilitate rapid mercury depletion events. Mercury serves no known biological function and exposure via ingestion can cause a variety of health problems in organisms. It is known to magnify as it passes up the food chain and bioaccumulate in individuals as they age. This may be especially pronounced in long-lived top predators, such as Adélie and emperor penguins. This study used feathers to investigate the influence of trophic position on mercury concentrations for these two species and between female and male Adélie penguins. This study considered the proximity of Adélie penguin breeding colonies to potential mercury sources and temporal differences in mercury concentrations and trophic position by assessing age-related differences and trends between 2004 and 2016. Emperor penguin feathers were higher in mercury than Adélie penguins and this is likely due to the higher trophic position occupied by emperor penguins. Male Adélie penguins had higher mercury feather concentrations than females, which may be because males are feeding higher in the food chain and/or because females have egg laying as an additional mercury excretory route available to them. Adélie penguins breeding in the southern Ross Sea had higher feather mercury levels than those breeding further north. While there was variability in Adélie penguin mercury concentrations across years, no linear trends were identified, nor was there a difference in mercury concentrations among adult age classes. This study provides important baseline data for future monitoring of mercury in Antarctic ecosystems and contributes to our understanding around the risk of dietary exposure in wildlife to mercury pollution.