Given the lack of background data on essential and non-essential trace elements in invertebrates and fish known to be the predominant prey of marine mammals and seabirds breeding at the Kerguelen Islands, this study intends to provide these results of great influence for predators in higher trophic levels. To this end, plankton organisms (9 species/4 phyla), mollusks (2 bivalves and 2 squid species) and fishes (8 benthic and 10 pelagic species) from Kerguelen waters were analysed for cadmium (Cd), copper (Cu), mercury (Hg), and zinc (Zn). Individual concentrations of non-essential elements (particularly Cd) showed larger variation in comparison with essential ones due to homeostasis. Cd ranged over 4 orders of magnitude; however, Hg ranged only 1, without significant correlation to trophic level. Instead, ecological parameters (benthic/mesopelagic habitat and feeding ecology) showed a more important influence on the results. Concerning seashore organisms, bivalves collected inside the Gulf of Morbihan had higher Cd concentrations compared to those from the Kerguelen shelf, suggesting a local source of Cd, such as runoff water from bird colonies. Comparison with literature showed metal concentrations in invertebrates and fishes from Kerguelen Islands somewhat lower than in the Antarctic area, with Hg prevailing in benthic species and Cd in pelagic ones. In contrast to Hg, Cd values of squids, jellyfish and the amphipod Themisto gaudichaudii were significantly higher than all other species. Finally, top predators foraging in this area that can be subject to potentially high Hg and Cd exposure through their diet at Kerguelen are reviewed.